Reunion
by SomewhereBeyondReality
Summary: Set directly after Season 5 ended. John meets someone who gives him hope again, hope he thought he'd lost forever. However that hope could either lead to a shining future or destroy both of them once more. J/E! First story in the 'Atlantis is Home' Series
1. Chapter 1: A Meeting and a Revelation

**Chapter One: A Meeting and a Revelation**

Colonel John Sheppard stood on the edge of the small balcony staring at the arching bridge spread out before him. He sighed and stretched out, his eyes scanning the horizon. They were back, Atlantis was here, they'd arrived 'home'.

So why didn't he feel like it?

It was twilight now, with the sky slowly darkening and faint stars beginning to show. Everyone else had headed to bed ages ago, the eight of them, him, Woolsey, Rodney, Ronon, Amelia, Teyla, Jennifer and Carson had sat on the pier for hours, talking, laughing and – for once, just letting life pass by. The Wraith Hive had been destroyed and the Earth was safe. He'd thought that was enough.

John clenched his fists, hunching over the cold railing as a wave of unexpected pain washed through him, almost forcing him to his knees with the power of it.

He'd killed Todd. Murdered him most would say. After the ally had come and warned them of the danger, after he had supplied the ZPM's that saved John's planet and its entire people he had just killed him.

John was soldier, it was his job to fight, to defend, to protect. He didn't lie in bed crying every night after he'd taken a life; if he did that it would have destroyed him a long time ago.

So why was he so bothered about Todd? He'd lied and betrayed and manipulated them, if John hadn't got to him first, would only be a matter of time before the Wraith returned to stab him in the back. Sure he'd done it in cold blood, not in self-defence or in the heat of battle or natural reflex. The action had been planned, coolly calculated but _HE HAD DONE THE RIGHT THING._

Or that's what he had to keep telling himself.

John closed his eyes, pressing his forehead against the rail, trying to erase the image seared behind his lids. It was done now, over. Whether right or wrong there was no way he could turn back the clock. If he could that wouldn't be the first thing he'd change.

"_I'm a killer," _he thought numbly, "_sure, I've saved a few lives but there's no way that could make up for everything else I've done."_

He stood there drowning in hate and self-loathing. He'd just saved the world_, _saved millions – _billions _of families, friends and loved ones, but that didn't change a thing for him, not now, not inside, because no matter how much you tried to make up for the mistakes of the past, it never left you. He'd learnt that along time ago.

John forced himself to think back over that revelation, when had it begun, when had the guilt and the doubt first begun to truly catch up with him?

After Afghanistan definitely, Nancy leaving had something to do with it, though he never realised that at the time. Maybe after so much time watching his friends get massacred before his own eyes, helpless to do anything about it was when it really hit home. Even in Antarctica – the wild, lonely, beautiful landscape of Antarctica – he had never been truly content.

Content...what an unusual concept. He hadn't been content for a long time, well...not on Earth anyway.

John's mind wandered back to that time after _leaving _Earth, the years in a war torn, blood-thirsty, hard and bitter galaxy. Fighting against enemies that would haunt most people's worst nightmares and battling terrible odds that would have most humans fleeing for cover.

He frowned, opening his eyes again though they were still fuzzy and out of focus, unable to believe what he'd known was true for a long time:

It was in those horrific, petrifying, mind-blowing, incredibleyears, that he – he'd...*_he'd felt content again.* _It was when he'd been trapped in a horror movie, in a terrifying dream, that he had begun to believe in himself again, to learn himself, to let things go...to _like _himself.

That just proved there was something wrong with him.

John refused to admit why he had gone spiralling downwards into the old catalyst of hate again, why he had lost that new path he'd been following and wandered lost and alone back to the other one. He refused to admit why, in the last two years he had once more began to become someone he loathed and detested. Why he had slammed the protective armour around his heart shut and rebuilt the wall surrounding it.

He knew but he wasn't going to admit it.

Faces flicked through his mind; air force officers, children, colleagues'. The faces of those he'd left behind; of those he'd failed.

His subconscious lingered on the last one longest of all, examining every detail that had been stored away in his soul, now it wasn't there for real life.

That facewas the reason he had become not the man who ended lives rather than saving them. If that face had still been there, now, beside him; then maybe just maybe he could be the type of man that did good for the world instead of evil. Who could love and live a life full of joy and not hate.

As it was, that future had been slowly dragged out of his reach as surely as she had been.

John shrugged and pulled away from his stance on the railing, he should probably head to his quarters, the team had been ordered to return to Stargate Command tomorrow; there was a lot of stuff to get through.

The next morning, SGA-1, Jennifer and Carson met in Woolsey's office, preparing for their return to America; even Teyla and Ronon had been ordered to attend the debriefing, not only to discuss the recent events but to sort out the future as well. What was going to happen to Atlantis now?

It was like being back at school with the teacher preparing for an inspectors visit. "Just remember," Woolsey was saying, "the IOA are extremely thorough, they will demand the reasoning behind each and every one of your decisions. Make sure you are prepared and don't give them any chance to catch you slipping up, because I assure you – they will try."

"Uh, correct me if I'm wrong," John began, "but until the last year, weren't you the one sitting on the other side of the table, demanding explanations for our actions?"

Woolsey coughed awkwardly and polished his glasses, "well yes, to a certain extent I was seeing looking at things from a slightly different, ahem, perspective. This gives me a rather, good experience of how these meetings are...managed."

John rolled his eyes and Ronon grunted. Woolsey frowned, "nevertheless I expect you all to behave with utmost propriety."

Teyla nodded reassuringly, "it will be fine Mr Woolsey," she promised him sincerely.

"Good, good," Woolsey paused and shoved his glasses firmly back onto his nose, "well," he said, standing up and looking each and every one of them in the eye. "I guess this is it then."

Almost four hours later John collapsed in his room with a groan. The SGC certainly didn't believe in going easy on you, not so much of a "_hey, hello, what have you been up to,"_ before shoving them all in a intimidating and scarily clean room with a long table that looked like it used a whole warehouses' supply of polish everyday just to keep it shiny enough for him to use as a mirror.

At least Sam had been there as well; softening the IOA's blows a little and Doctor Jackson had turned up halfway through which made thing more interesting but even so... they'd just saved the planet, couldn't the damn people cut them a bit of slack?

John thumped his head on the pillow and stared at the blank grey wall, wishing he'd brought his Johnny Cash poster.

On the bright side at least he'd been given the afternoon off, so they could get used to being on his "Home Planet" again. John unzipped his backpack and reached for a scrap of paper shut inside the rather battered copy of War and Peace. He glanced at what was written on it and headed for the door –the team could eat lunch without him today; there was something he had to do.

And it might take a while.

Late that afternoon he drew up outside a large, stately looking house opposite a park, it spoke of money and wealth and prestige, but looked welcoming as well; built in large warm coloured bricks and a sweet smelling wood-panelled door with a silver knocker, carved into the shape of a bear. The small front garden was a riot of flowers and the hedge was perfectly trimmed, with a small black iron gate set deep in the middle of the thick green leaves. He swallowed and got out, fiddling with his trademark Atlantis military jacket. He really should have changed before he left – and done something with his hair. "Still, here we go," John muttered to himself, slamming the car door shut.

The first person to greet him at the door was actually a large white dog, "Hey boy!" He said in surprise, automatically bending down to ruffle his ears, "you're Sedgwick, I'm guessing."

"You've obviously heard of him then," a voice above him said.

John swallowed and stood up awkwardly. "Mrs Weir?" He said. "Uh, I worked with your daughter, Doctor Weir. My name is–"

"Lieutenant Colonel John Sheppard." She finished for him, a slight smile hovering around her lips. "Do come in, it's rather cold out there and Sedgwick looks like he's eager to make a new friend. I'll put the kettle on and he can use your feet as a hot water bottle."

John glanced at Mrs Weir as she poured them drinks. She was quite a short woman but still cut a striking figure in her black trousers and cashmere sweater. Although her skin was wrinkled it was creamy and soft with grey hair framing her cheerful features; neat, cut short and not a curl out of place. But it wasn't only in the hair that he could see the resemblance to Elizabeth. Both of them had the same perfect poise and fluid grace when they walked, that inner confidence that you just noticed, though they seemed unaware of it. Mrs Weir was older of course but hadn't lost the self-assertive dignity that you could read in every detail of her posture. He swallowed a lump in his throat; sure that Elizabeth would have aged with just as much grace as her mother – if she'd had the chance.

"Out of curiosity," John asked, tearing his mind away from unwelcome memories. "How did you know who I was?"

Mrs Weir smiled as she passed him a mug, "my daughter mentioned you, you know – in her letters. You were obviously working quite closely together and she admired you greatly, though you do squabble a lot with a certain Rodney McKay."

John grimaced, "There was no hope in keeping that quiet I guess," he said.

Mrs Weir laughed, "It sounded like Elizabeth had her hands full making sure you two kept out of trouble. She could never tell me where she was of course, or what she was doing, but believe me; the stories I heard when she visited!"

John smiled uncomfortably, astounded that she could still talk so openly about her deceased daughter; he'd expected his visit would trigger resentfulness, pain, grief, even blame, but she seemed quite calm and composed, perfectly relaxed to be talking with him.

"Trust me, she had her diplomatic skills stretched to the limit when she was dealing with us," he sighed.

Mrs Weir's lips quirked, "I'm sure she managed. My Elizabeth always had a scalding tongue on her when she needed one."

"I experienced that first hand,' John admitted, "but...she...she _dared _to negotiate with the most unexpected people." He paused, remembering the Genii.

"That was her." Mrs Weir agreed. "I always knew she was destined to go into politics one day, she was argumentative even as a child."

"I can imagine," John replied, grinning slightly, "Every time we got into an argument I found it hard to keep up with her it got so confusing. Sometimes I had absolutely no idea what she was talking about, just that it sounded good and she was probably right – as always."

Mrs Weir let out a low chuckle, "I know what you mean," she said, "She could take her father on by the time she reached fifteen." She sighed and gazed into her tea, swirling in the cup, "I miss her so much."

John's heart sank; they'd reached the point that he'd hoped he could avoid. He took a gulp of his drink, unsure of what to say. "I miss her too," He whispered, "A lot of people do." He stopped and went on uncertainly "and uh, I just want you to know, that I really am sorry about your loss. She was an incredible woman and nobody regrets her death more than I do." He clenched his mug, "but trust me Mrs Weir, Eliz – Doctor Weir is remembered."

Mrs Weir poured herself another cup of tea; "I wondered when we would reach this particular issue." She said, scratching Sedgwick's head. "Sweetheart, I'm not quite sure how to put this but;" She paused, "my daughter isn't dead."

John gripped his mug tighter; he'd seen this before, in the families of soldiers who had died in battle: Denial.

"Mrs Weir –" He started. But she cut him off.

"Caroline please." She said firmly, "Now I know what you're going to say: that I'm refusing to believe the inevitable and sticking my head in the sand, hoping all the troubles will go away. Many other people have told me the same thing, but I know what I feel. Elizabeth isn't dead; if she was I would be able to tell. My daughter is still alive Colonel and she will come back; against all the odds. Trust me."

"With all due respect Caroline," John said quietly, "I saw her death with my own eyes. There is no possible way she could have survived; otherwise, I would have saved her."

The woman opposite him narrowed her eyes, "I notice you don't actually say what your true feelings are about the subject, just what you saw a proof." She stopped and sighed, "Sweetheart; I can tell you were close to Elizabeth and cared about her deeply and she obviously felt the same way about you; so I am telling you Colonel. Don't depend on your eyes as the only source of truth."

She stopped briefly again and continued. "Dear, I'm going to tell you something that very few people have heard, so listen carefully." She sipped her drink, gathering strength. "A while ago, when my mother died, I knew she was gone; aware of it before the news even arrived. Don't ask me how, but I just felt that she'd left me, had been sent, as they say; to a better place. It wasn't easy but I mourned and I grieved and moved on. However when a Doctor Daniel Jackson and General O'Neill came and told me that Elizabeth had been killed I felt nothing. Not like I had lost part of myself, not that there was something missing, just the same as ever. That is how I know Elizabeth isn't dead."

"But –"

"I don't care what you saw," she said, her voice sharp, "I don't have any knowledge of what she was she was doing at the time or how she was lost but that is all she is; lost. And she will be found. Maybe she might even work with you again, I'm not sure. But my daughter will return, and –" here Caroline leaned forward slightly.

"And I think that deep down you believe that too Colonel, I've seen it in your eyes. Don't give up on her yet. You said you would have saved her, well you still can, instead of waiting for her to return, bring her back, she's out there, we just have to be patient and trust her."

John opened his mouth to say something but nothing came out; he shut it and looked at the carpet. She was Elizabeth's mother alright, the only person ever been known to out-argue him and leave him speechless.

"I'll go and make us another cup," Caroline said, sounding slightly embarrassed. She left the room leaving John deep in thought.

They talked for a while longer, relieving memories of Elizabeth. John told what he could of what she'd done in Atlantis without revealing the exact location and details and Caroline accounted endless stories of her childhood. Indeed everywhere in the house there were signs of Elizabeth. Photo's, pictures, awards. John fought hard to keep down the still-constant lump in his throat; in time maybe she would have shown him this herself. She'd spoken a little of her family and been sensitive about his obvious silence around his, but now he wished with all his heart he'd asked more, offered more. But it was too late.

Wasn't it?

When he finally left a couple of hours later with Sedgwick twined around his legs and promises to come back soon, Caroline whispered in his ear. "Remember what I said Colonel. She'll come back; you just have to open up that military mind of yours." She kissed his cheek lightly, "think about it."

John did think about it. Obsessively. On the whole long drive back to Stargate Command, the thoughts and conflicting emotions whirled around in his mind. Making his head ache, and heart bruised from beginning to beat again at a speed it hadn't reached for almost two years, fuelled by suppressed hope. He plodded along the quiet corridors, barely replying to the rare greeting, unable to shake of the words pounding through his brain _"she'll come back, she'll come back, she'll come back..." _

Curled up in bed hours later they were still playing over and over. It must be past one now and John still couldn't sleep. He turned over and gazed up in to blackness. It was all wrong. In Atlantis there was always light and sound, reassuring and steady. The glow of the twin moons would shine through the flimsy curtains and clear windows making flickering shadows on the wall and ghostly silhouettes on the carpet. Some would find it unsettling even spooky, but John could watch for hours. The noises, irritating at first, but once you got used to them like a song playing in the background, mostly unnoticed though unconsciously enjoyed and when shut off; sudden, abrupt loss.

Here it was different. Black and silent. Like a tomb. No windows to show you the whole world out there, that you weren't totally alone and forgotten by everyone. No breath taking views that could refresh you in just a short, snatched moment.

And no balconies. If John really couldn't sleep when he was back in Pegasus he would always crawl out from under the covers and pad out to one of the many decks. He would lean against the railings, his hands gripping the cold metal and gaze out over the ocean; a gleaming sheen of pale silver, sparkling subtly under the dark night. He could see Atlantis's smooth reflection, as if it was floating on a moving mirror, identical except for the faintest ripple, causing the image of sturdy towers and lighted windows to shimmer and he would realise actually, all of it, every building and pier and spire was as insubstantial as mist.

Looking up at the patterns of glowing lanterns of light amidst the blackness, John would play the game he remembered from childhood, making shapes and pictures from the stars. He used to pick the stars and name them after his family, giving one to his brother, one to his father and one for his mum before moving onto friends and extended relatives. His father had taught him the constellations, the Greek myths and legends and John would recount the stories; Orion, Pegasus of course. And Andromeda.

She'd always been one of the most famous, the story of a princess so beautiful and pure that the jealous sea god had ordered her to be chained to a rock and left her to the wild oceans. Everyone gave her up to death before a young hero; Perseus struck by her beauty saved her and flew her away.

Now John had started to do it differently. The Ancients had made their own constellations of course, but something both he and Rodney had agreed on was how bad they were at naming things. So on those quiet, silent nights John would create his own. Take stars and planets (some which he had been to) and form a tapestry in the sky.

There was one constellation though, that John's eyes strayed to more than others. A cluster of stars which seemed – to him – to form an outline of a woman. Graceful and slender with bright eyes and flowing hair. The name had chosen itself. _Elizabeth. _

John wasn't a storyteller but that constellation had come with a history of its own. A story of a life that told of adventure and discoveries and courage and friendship. Some would say it was a tragedy but to John it was a legend. And as long as she was there, hanging in the sky, looking down on him, John could feel peace. Looking up at her, at her profile he could feel pure, perfect joy that he had rarely felt anywhere else since Elizabeth had left.

Elizabeth wasn't here though. Not in the SGC, though John knew she'd been commander there. And not anywhere on Earth.

He'd lost her, left her behind, abandoned and alone in Pegasus. And now he was suffocating under the mound of Earth, burying him in mind and body.

"_She'll come back, she'll come back, she'll come back..." _"Shut up!" He groaned, banging his head on the pillow. She was gone. She was never coming back. He thought he'd accepted that by now. He'd failed. And she was dead because of it. He may never forgive himself, but he thought he'd allowed himself to give up.

Because that was easier than to keep hoping.

Yet now, thanks to _her mother, _that hope, which he thought he'd finally stamped out, was blazing anew.

"She'd dead!" John told himself, "she'd dead and she's not coming back." He turned over once more and settled his head on the pillow, willing sleep to overtake him.

It didn't. After barely a minute John gave a desperate sigh, flung the covers back and struggled out of bed. Stumbling across the floor he flicked on the switch and blinked in the harsh light that flooded the room. "I can't believe I'm doing this," he muttered to himself as he grabbed his bag and rummaged around inside. Drawing out his copy of War and Peace yet again he flicked through it feverishly, until he found what he was looking for – it was amazing how much stuff he had hidden in here. The piece of paper was even more worn than the last, though less crumpled. John sank down onto the bed again and stared at it wordlessly.

It was a photo of the Atlantis team; taken just after they returned to the city after first the Ancients, then the Replicators took it. They'd just dragged all their stuff back in and were in the midst of unpacking; John remembered that even Rodney grumbled less than usual about all of the "heavy labour." Zelenka had whipped out a camera and insisted of taking a photo of the return.

The gate stood behind them solid and unmoving, even after everything it had gone through; Ronon was leaning against the outer edge of it, still talking to Teyla and trying to ignore the lenses while Radek yelled at him in Czech to look in his direction.

Teyla was on the inside of the arch, bending over to lift one of the boxes, her vivid hair flung over one shoulder as she glanced over at the camera, her face lit by a small smile.

Rodney and Carson were crouched in front of Ronon; attempting to clean up some equipment Rodney had spilt in a rare effort to help, there were papers and folders everywhere and both of them wore mixed expression of amusement and irritation as the flash of the camera caught them by surprise.

John's eyes trailed over to the other side of Teyla, under the centre point of the Stargate's perfect curve, where he and Elizabeth were. You could tell the sun was setting outside the gate room, shooting through the surrounding windows so golden rays of sunlight danced and criss-crossed around them so they looked as if they were floating in a beam of light. The two of them were standing close together and facing Radek but obviously pausing in the middle of deep conversation. Elizabeth was laughing, her head tilted up slightly, so you could see the sparkle in her clear, green eyes and glint of her glossy hair, spilling down over her shoulders. He was grinning too with obvious satisfaction, his face missing the deep bags under his eyes that had become a constant land mark now.

John's eyes stayed on that image for a long time, drinking in every detail of the perfect joy in that captured moment until his vision blurred and his eyes stung. He blinked, still focused on her laughing face.

The horrific truth hit him once more; pain overtook his entire mind, crippling him.

Elizabeth wasn't coming back.

Tears began to build up in his eyes and he hurriedly blinked them away. "Shut up John!" He hissed furiously, "There's no point crying about it now!" He ripped his gaze away from the photo and closed his eyes, blood drumming in his head. What – what if Elizabeth's mother was right? What if Elizabeth _wasn't _dead? That she could come back? Stranger things had happened; Carson for instance, killed in the explosion and then returned to them in the form of a clone. Ronon, no one could quite explain was happened there. He'd read mission reports of the Gou'ald sarcophagus, a box that literally brought back the dead. Even he, himself, fed on by a Wraith and then given the years of his life back he was so sure he'd lost forever. Was it so improbable that Elizabeth could make it too?

For a moment John allowed himself to imagine it; Elizabeth returning, taking control of the city again, moaning at him about finishing all his paperwork. Even that vision seemed idyllic compared to now; she certainly didn't whine as much as Woolsey.

No. John couldn't depend on that. He couldn't waste his life waiting for her; he didn't want that and she wouldn't either.

So...what if he didn't have to wait for her? What if he could go and get her himself? John had never been one for just sitting there; thinking, theorizing; that was Rodney's department. He had to do something; actions not words. So what could he do now?

Once that thought had taken hold of him he couldn't let it go; there had to be a way, there always was. He just had to find it.

John leapt up and paced up and down the small room, his mind spinning out of control, running through the possibilities.

They'd met her clone, the year before last. It – she was dead though, had to be. Could there be anymore out there? No. Impossible.

Her real body was destroyed. The replicators had transferred her consciousness into a different form. She'd then abandoned that when trying to ascend. No way of getting either of those back, besides it was her he wanted; not the empty shell.

She'd hacked into Atlantis's system and built FRAN, which had been a replicator. John had never been sure it was really her right until the last minute; but the look in her eyes as she stepped through the gate, told him it was really Elizabeth behind those alien features. That body was frozen out in space. Useless.

Racking his hands through his already messy hair, John slumped against the wall. "Happy now?" He raged to himself, "All you've done is proved to yourself how completely and utterly *dead* she is. Even Rodney can't figure a way out of this and you know he's tried, why do you think you could all of a sudden?" He slid to the floor, staring at the grey carpet.

Suddenly it struck him; so totally and utterly obvious that he couldn't believe no one had thought about it before.

Elizabeth was a replicator. Yes she was stuck in space but that didn't mean she was dead. Right now, she was a machine, and for a machine all you had to do was turn it on...

He sat up, his fists clenched. Would it work? Was that it? All they had to do was reactivate her nanites? John thought back to Niam. They'd done the same thing with him when he'd been sucked out into space and Rodney had reactivated his nanites. He'd been too easy to wake up in fact.

"Alright then, if it's so simple, why hasn't this come up before?" Another part of his mind asked. John was silent, still for a minute. He knew why. They hadn't wanted too. She'd come and gone so many times now; no one could take it anymore. They'd just shut down and abandoned her.

Including him.

John sighed and ruffled his hair again. A sudden calm had come over him though his heart was still racing. He was going to get Elizabeth back. Sure he'd have to face up to Woolsey, the IOA, General Landry, heck even his own team. But dammit, he would try. He yawned, suddenly exhausted, mentally and physically. He glanced at the photo again and smiled, flicking off the light and climbing into bed once more.

He was going to bring Elizabeth home.

For the first time in two years, John Sheppard went to sleep with a smile on her face.

She was coming back.


	2. Chapter 2: We Don't Leave Anyone Behind

**Chapter Two: We Don't Leave Anyone Behind**

Nearly a week later John sat slumped in the mess hall, debating inwardly on quite how he was going to open up this certain rather sensitive topic of conversation. They'd been back on Atlantis a couple of days now , which – thanks to three fully powered ZPM's – had just yesterday left Earth to take a fast but relatively quick trip to a uninhabited planet nearby, covered almost completely by ocean. In the end, the practicalities of keeping Atlantis on Earth, (i.e. the damn cloak never actually being able to turn off without giving everyone in the harbour a heart attack and only having being able to use one gate at a time,) never really worked out. So he'd got to sit in the cool, glowing chair again, and feel really special piloting the largest space ship ever known to man.

And John had to admit, he'd enjoyed being able to look out the windows again without some random guy in boat staring straight over in his direction, (Yeah, he knew he was invisible but...it was just weird.)

"Alright," he thought, dragging his mind back to present day, "here goes."

"You're planning to WHAT?" Rodney yelped, spitting out his mouthful of broccoli and chicken, John wrinkled his nose at the sight of it. Seriously, couldn't the guy consider that some of them were actually trying to enjoy their food?

He took a sip of his drink praying for calm. "I said Rodney, that I'm planning to reactivate Elizabeth's replicator form body, her, 'FRAN' one." He reached over for the ketchup and squirted it over his pie trying to look nonchalant and relaxed but absentmindedly drumming his other hand on the table even so. John risked a glance at his team. Rodney was just gawking at him, his mouth slightly open. The normally controlled Teyla had a troubled look in her soft brown eyes and was frowning, creasing up her forehead and even poker-faced Ronon's gaze was fixed on him. He coughed and looked away. "What?"

"What do you mean what?" Rodney blustered, "you've just informed us you're planning to carry out one of your ridiculous, ill-considered, hair-brained, and not to mention unauthorised, impossible idea's and you just expect us to take it lying down?"

John leaned back, "Rodney, stop overreacting. Ridiculous? Yes. Ill-considered? Yeah probably. Hair-brained? 'Course. Unauthorised? Most likely," he listed, ticking them off on his fingers. "But impossible? No. Reactivating her nanites should be simple."

Teyla cut in before Rodney could go off into a rant again, "Colonel, I do not understand why you wish to go and rescue her now? It has been almost a year since she sacrificed herself to destroy the last of the replicators. Why have you made this sudden decision?"

John shrugged and took a mouthful of food before answering, he chewed, swallowed and then shovelled some more into his mouth, gaze fixed determinedly on his plate. "Sheppard?" Ronon grunted as the pause stretched out longer and longer and it became obvious he wasn't going to reply.

"What?" He asked, not meeting the Satedan's penetrating eyes.

"What's changed?" He growled. "It's been ages."

"I don't know what you're talking about," John said nonchalantly, avoiding the stares he knew the other three were giving him right now.

Rodney suddenly clicked his fingers, "something happened when while you were back on Earth didn't it?" He exclaimed triumphantly, "something that caused you to come up with this crazy plan!"

"And what could possible haven happened while I was on leave that would want me to go and rescue Elizabeth Rodney?" John asked, "Seriously buddy, your conspiracy theories suck."

"No," Teyla said eyeing him thoughtfully, "he is right. This is not usual for you."

Ronon grunted in agreement again, "something's happened."

John could begin to feel his temper mounting and he struggled to rein it in, he'd been expecting this after all; After hardly mentioning Elizabeth for months he'd just come up out of the blue, and announced he was going to go and get her. Of course the team would notice.

"Whatever," he said brushing it off, "Teyla, we were planning to gate back to Pegasus in a couple of weeks anyway right? To see your people? If we take detour – I'll talk to Woolsey –"

"TALK to Woolsey!" Rodney cried, his voice getting high and shrill, "Sheppard are you out of your mind? What are you going to 'talk' about? You can't just waltz into his office and tell him you're going to go and bring a dangerous and out of control replicator back to Earth!"

"This is Elizabeth, we're talking about here," John snapped. Rodney just rode right over him.

"Even if he does authorise it and I put emphasise on the 'if' there, how do you think Stargate Command, the IOA, Homeworld Security and the Pentagon are going to react? Oh, yeah sure, go right ahead, do what you want, I mean its not like last time she showed up there was any trouble, right?"

"Rodney –" John began only to be ignored again.

"In fact I don't even get you, when she was first hit by that beam weapon and the only way to save her was with the nanites you were the one refusing to do it. If I remember rightly, it was Jennifer and I who came up with that and saved her behind your back. When she and the others hacked into the computer last year, you were as suspicious as the rest of us; that she was a threat, that she wasn't who she said she was. What's happened to the cities safety and security now huh?" Rodney paused, bright red in the face and breathing heavily. "Go on, tell us."

John leaned forward, his face dark with anger, "And Rodney, if I remember rightly, you were the one who would go to any lengths to bring her back too, so what's changed for you? Too hard? Too risky? Scared of getting into trouble?"

"No,' protested Rodney, "I just –"

"You said she'd do the same for me," John said, the fury mounting to an almost uncontrollable level as his voice echoed in the large mess hall, "well I am. I thought you'd agree with me. But you don't." He scraped the chair back and stood up, almost spitting with rage, if he couldn't depend on his team, who could he trust? "Sorry to have bothered you."

He began to walk away and Rodney gave an exasperated sigh. "Sheppard come back!" He yelled, "Stop acting like a –" There was a loud thump and slight cry of protest. Ronon had obviously shut him up just in time. Even though he knew he was over-reacting John kept walking, driven by an almost inhumane ambition. He needed to see her again.

And he wasn't going to give up until he did.

Rodney was holed up in his lab, examining an artefact SGA-3 had found somewhere offworld when Teyla and Ronon walked in. Rodney glanced up and kept working. He didn't want to talk to them. He knew what they'd come to say. As far as he was concerned; Sheppard was an idiot, he was the one who should come and apologize, they shouldn't have to go and make it up to him like he was the one who'd actually done something wrong.

"Rodney?" Teyla began after they'd stood there in silence for over a minute.

Rodney gave an absent, "mmm", still not willing to give up trying to ignore them.

"Rodney." Teyla repeated this time it wasn't a question, it was a statement.

He groaned and looked at her, "what?" He snapped.

"We must talk about this," she said, glancing at Ronon for support, he grunted in agreement.

"Oh, talk about what?" Rodney grumbled, "Unlike some people here, I do actually work. My job is important. And I've never really seen the point of –"

Teyla slipped onto the stool next to his, "you know what I mean Rodney. John. His...proposal." She paused and her voice got lower. "Elizabeth."

"Oh," Rodney said cringing involuntarily, "that."

They sat in silence for a minute before he broke it, staring at the ground and slowly turning red in the face, "Well, it's obvious something happened when he went back that triggered it."

Teyla nodded her face serious, "maybe," she said, "but I have a feeling this has been building up for a while. He has always said he never left people behind, why should Elizabeth be the exception?"

Rodney snorted, "Because last time she turned up she was a high-level security risk, Sheppard knew that."

"Since when has Sheppard been one to follow the rules?" Ronon asked, looking bored. There was a long pause, Teyla breathed deeply, there was something none of them were saying and they all knew it.

"I believe this goes deeper than he's showing," she said slowly, "he misses Elizabeth, it has been almost two years since we lost her; he was closer than any of us. Think about how hard it must be. Last time, he hid all of that behind his authority, now...He obviously regrets that." She stopped and went on, "but we know John, he's not going to give up and none of us would expect him too. I am almost surprised he took this long to find a way." Teyla let out another whispering sigh, "but maybe he didn't want to," she finished under her breath.

"But how do we know it's really her?" Rodney asked with frustration, "I mean it could still be a replicator in there, we could be putting everyone in the city in danger."

Teyla met his gaze, "I believe that – after she gave her life for us – you also seemed sure it was her Rodney."

"Does it really matter?" Ronon shrugged, "he wants to get Weir back and he'll find a way, why are we all so against that? Sheppard was right about one thing McKay; after she got hit the first time you were as desperate to get her back as he was. And Teyla's right too, he'll do what he wants." He turned away again, tired by the long statement.

"Yes, yes, we get the point," Rodney complained, "we're either with him or against him." He gave another groan.

"Elizabeth was our friend too," Teyla said quietly, "when she came back last time, we were all so suspicious of her – and she saved our lives." 

Rodney swallowed, "yeah."

Woolsey gazed at the four expressionless members of SGA-1, standing ready to beam. He still couldn't quite believe he was letting them do this. Letting them rescue a potentially dangerous replicator was beyond insanity. What was he thinking? He resisted the urge to call the mission off and land the Deadalus, held in the desire to cut everything and send the team back to their offices to file mission reports. He took a deep steadying breath and his poker face held.

If he was going insane (and he was seriously considering that possibility now) at least he has Sheppard's team to blame, they could pay for psychiatric hospital. Since Sheppard had returned nearly a fortnight ago he'd been stubbornly insisting that he go back and reactivate Doctor Weir's replicator body. At first Richard had turned him down flat out, was that man already crazy? (Short answer – yes, almost everyone who'd been to the Pegasus galaxy was.) However the Colonel seemed unstoppable, he'd ambushed Woolsey in the mess hall one day and listed all of the assets Doctor Weir had to offer Atlantis, her leadership abilities, her fluency in Ancient, her previous experience at Stargate command, her knowledge of the city, her negotiating skills, it was like he'd memorized everything in her job original referendum. Richard had almost run back to his office still shouting obstinate no's behind him.

A couple of days later, Doctor McKay and Doctor Keller walked into his office with the list of names of people offering to come on the mission to rescue her. This included almost everyone in the city, half of SGC staff and even some former Atlantians. The damn thing was pages long.

The next week Ronon virtually kidnapped him to practice sparring, for 'self defence.' Richard shuddered to think who he was meant to be defending himself from. However while his whole being was focused on trying to duck the hard sticks that kept swinging towards his head, Ronon was quite able to keep up a (mainly one way) conversation. It was ironic that this time the usually silent warrior was doing all the talking. When Richard managed to pant out what a good job the Satedan been doing at training people, he'd replied that he was only here because it was Elizabeth who'd convinced him to join the team. After a few more swipes he casually mentioned the one time when Elizabeth had saved Earth and the city from a vicious Wraith attack saving billions of lives in the process. Next it was the occasion she'd negotiated with the Genii, or managed to retrieve Sheppard from a time dilatation field. Teyla had mysteriously appeared to watch and started to chip in with stories out how she'd single-handedly managed to hold the city together in the first year.

By the time Keller and Rodney turned up, he'd been subjected to every single thing Elizabeth had done while on Atlantis, every difference made, every decision, every time she'd prevented the city from collapsing, every life she'd saved.

Thinking back, Woolsey still wondered how his restraint had held up until then, what had broken him, happened later. Sheppard returned from an off-world mission and after obviously having heard the whole story from the other four, stormed straight to his office.

"Dammit Mr Woolsey, what else do we have to do?" He asked through gritted teeth.

Richard coughed and arranged some papers, "Much as I admire your – persistence in the matter of Doctor Weir's um, resurrection, surely you _must _realise it is impossible to attain security clearance for such a rash action." He replied smoothly.

"C'mon Woolsey, you know how it works, there are some people who can pull some strings. You've just got to find them."

"Colonel," He snapped, would he ever get him off his back? "Believe me, at this moment I would like nothing more than to give you what you want, if only to earn a moments peace, but rules are there for a reason. If you know of any people in positions of authority who do actually agree with you, then I MIGHT be swayed, but until then –"

"Colonel Carter, Doctor Jackson and General O'Neill." John answered without missing a beat, Richard looked up. "If you need support, they're it," he explained.

Richard frowned; he hadn't actually expected him to come up with anything. He gave a silent moan and rubbed his eyes. "Colonel, I truly understand your loss, really I do, you were obviously close to Doctor Weir..." Sheppard's expression darkened and Woolsey continued hurriedly, "but there is nothing I can do. I'm sorry." He turned to his laptop, indicating this topic was over – for good.

Sheppard stood up, "Woolsey, if you don't let me getDoctor Weir back_, _then I resign. But before I leave I promise you, I *will* rescue her, even if it's by myself, alone and without your authority." He leaned on the desk, "She sacrificed herself for us, and I'm finally doing something about it."

It was in that moment, when Richard saw the hard, desperate look in his eyes that he gave in. He wasn't stupid, he'd been taught how to read emotions and everything about Sheppard right now was screaming that this was a man who was on the boarder of madness. He was going to get Weir back and there was nothing Richard could do to prevent him.

So he gave up. A few calls to Earth, a few compromises made, a few pulls at the strings that Sheppard mentioned and it was sorted. He had a feeling O'Neill had intervened personally but for once, he wasn't going to complain. And now they were off.

Woolsey nodded once to the four unreadable faces of his best team and tapped on his radio, "they are ready to beam." The next instant they had vanished in a blinding flash of light and he was alone in the gate room.

It was up to them now.

John piloted the Jumper in a smooth curve, circling the gate. "Look, there they are," Rodney said, pointing to white, motionless forms, floating out in empty space. John swallowed at the sight of them; trapped, stuck, frozen forever; he guessed that was as dead as machines got. John manoeuvred the Jumper around them, his eyes searching for Elizabeth.

"Over to the left," Teyla said softly.

"Make sure it's her," Rodney whined, "the last thing we want is to pick up the wrong one."

John rolled his eyes, "yeah, because I was really planning to do that." He hovered slowly towards the body, hearing the faint vibrations as the back Jumper doors opened. Angling the Jumper down slightly, he backed up. Carefully...carefully... There was the slightest of thumps, gently rocking the Jumper as her body landed on the floor. "Got her!" He said in relief.

"You sure?" Rodney asked, tapping on the console, "Ok, ok! Just checking," he said defensively as John shot him a look. "Let's just get out of here."

They had already visited New Athos first, many of the crew on the Deadalus also eager to see the Athosians. Inwardly John had been subdued at the thought of losing Teyla as well; she was considering remaining behind in Pegasus with her people. However on arriving at the planet had been a shock; just the week before a hurricane had hit the Athosian settlement, killing and wounding over a dozen. Teyla's horrified eyes as she had seen the damage done to her people had been something John wouldn't forget for a long time, and neither were her desperate screams as she searched for Kanaan and Torren among the injured.

After discovering both of them were fine and well John had wondered selfishly if this meant the end to any hope of Teyla returning with them to Earth. He couldn't blame her; she needed to be with her family. However one genuine blessing came out of the whole ghastly mess. The Athosian settlement had suffered so much in the recent tragedy and after already losing so many people under Michael's horrific experiments they needed Atlantis's support more than ever. As Teyla had told the team, they were weary of the struggle and pain they had endured, some were even beginning to believe they were cursed, that the Pegasus galaxy was determined to make them suffer for some past misdeed. They needed a new start, fresh hope, and a future again. In the Milky Way if need be.

So they did. With so few left it wasn't hard to transfer them and their belongings to the Deadalus; Colonel Caldwell was unusually accommodating after Earth granted permission.

As Rodney commented wistfully, it was nice when things worked out as easily as that.

Elizabeth remained unconscious in the prison cells on the whole journey back to the Milky Way. Once there; the team gated her in the Jumper to a small abandoned moon; this had been part of Woolsey's agreement. They could reactivate Elizabeth's nanites, let her build a new body, make sure she was completely safe to be around and then return to Atlantis.

"That's it," Ronon said gruffly, dumping the last of the bags in the room. John nodded absently, laying Elizabeth/Fran (he'd never get used to that, and was glad he didn't have to) on the bed. There was an abandoned village just a few miles from the gate; people had obviously left, fleeing from the Gou'ald, Ori or some other enemy. The houses were a little bare and cold, but they had some furniture, were reasonably sheltered and weren't blown to pieces, like a couple of other places they'd considered. Even if Rodney did complain about the 'medieval standards.'

Right now the doctor was hunched over his laptop, making no effort to help the three of them carry the stuff from the Jumper. "McKay?" John said questioningly, turning to him.

"Yeah, yeah, I'm almost done." He replied, flapping his hand.

"You know you didn't have to do that the moment we stepped through the door," John said, grabbing some water.

"As far as I'm concerned, the less time we spend here the better," Rodney grumbled, "we'll be here ages, while she builds her new human body anyway, I mean look at all that stuff," he gestured to the materials, spread all over the floor.

John shared a glance with Ronon, "yeah, that heavy, heavy stuff that we all worked so hard to bring in." He snorted.

"Whatever," Rodney brushed the comment away, "to be honest this is so basic by now. I mean I'm sure um, lesser brains would find it a serious challenge, but as it's my second time, well, lets say like stealing candy from a baby." He gave them a smug smile.

"Yeah, so basic we're all still waiting." John muttered under his breath. He flopped down against the wall, ripping away the packet of a snack bar.

"Ok, done!" Rodney announced a couple of minutes later, "her energy signature is very weak, the obvious result of being frozen in space for a year but I think I can reactivate these replicator cells with very little difficulty." He looked round at all of them, "hopefully."

John stuffed the last of the food in his mouth and stood up, he nodded to Ronon and Teyla, who took up defensive positions around her body; guns poised.

'We're absolutely sure we want to do this," Rodney said nervously, his gaze darting between Elizabeth and the laptop.

"Well, no actually I'm having second thoughts," John answered seriously, a look of utter shock passed across Rodney's face.

"You've got to be kidding! After everything you put us through –"

"Yes Rodney, I'm kidding," John rolled his eyes at Ronon. "Now can you just go?"

Rodney gritted his teeth but was silent; he tapped a few keys and then closing his eyes, pressed down on the enter button.

Nobody moved. All gazes were fixed on the replicator form. Rodney sneezed once and then snuffled uncomfortably, Ronon's fingers flexed, Teyla swallowed. John didn't budge. His whole being centred towards her. There was utter silence for another long moment and then, so slowly it was almost unnoticeable; Elizabeth's lashes fluttered. Once or twice, three times. John's breath hitched and his stomach squeezed tight. Then, giving a soft moan, her eyes flew open.

They flickered, at first registering shock and even horror, but as they darted everywhere, taking in the whole room, scanning Ronon, Teyla and Rodney before finally resting on him the expression changed to concern.

"John," she said in a soft whisper, "I'm going to kill you."

A smile spread across his face.

She was back.


	3. Chapter 3: As Effortless As Breathing

**Chapter Three: As Effortless as Breathing**

"I still can't believe what you've done!" Elizabeth snapped, staring at the four of them. It was strange how – although it was Fran standing there in the middle of the room – there was something remarkably similar about her flashing brown eyes and locked fingers that were twisting together in agitation. "After everything that happened last time, I thought we agreed to _let things be._"

Rodney gave a shrill, nervous laugh, "don't look at me, it was his idea." He said quickly, edging away. "I told you!" He hissed to John, "It was what she wanted as well."

Her gaze flew to him once more, "John?" She demanded.

He fumbled awkwardly, shifting from one foot to the other, "well uh, um...it just kind of came to me and it seemed like a good idea at the time, so..."

"A good idea at the time!" Rodney interrupted, incredulous. "I'm telling you, he literally beat us all into it, Woolsey's still got the scars."

"McKay, shut it." John growled. Elizabeth narrowed her eyes and took a step towards him; instantly Ronon and Teyla leapt forward, guns raised.

Elizabeth glanced at them, "you still believe I am a security risk then?" She said. There was no sadness in her voice, blame or complaint, just resignation.

"Yep," Ronon replied, tightening his grip on the gun.

"Do remember that when you arrived previously you led a group of replicators to our door," Teyla answered, her voice unusually cold. "And lied to us."

A small smile flitted across Fran's face, "at least you haven't completely lost your senses then." She turned back to John, "What. Have. You. Done?" She asked, her voice clipped.

"I just told you," he said defensively, "a while ago I realised that if we went and found your replicator body out in space, then we could reactivate your nanites – like with Niam." He shrugged, "uh, so we did, it was pretty easy. Rodney's just jealous because he didn't have the idea."

Elizabeth folded her arms, "John please don't patronise me by pretending it was that simple, I don't even want to imagine what you had to do to the SGC to get them to agree with this," she paused, "assuming they did agree to this? Do you even have authorisation? Why aren't we back on Atlantis?"

"Why do you always assume the worst?" John asked dryly, "don't worry we haven't all gone AWOL. Besides it's not as if we're not prepared," he gestured at the loaded P-90 he was holding.

Her lips pressed together, "Do you really believe that would prevent me from attacking if I decided to?" She threatened.

"But you're not," John countered, "and you saved our asses last time, figured it was time to return the favour. But we're not back on Atlantis because yeah, you're still a serious threat. Don't think I'm underestimating that, even if you _are _Elizabeth Weir inside her...that..." He paused for a moment, his lost on what word he could possibly use, "...thing, you could still be compromised. But right now I'm willingly to take that risk."

Elizabeth raised one eyebrow, yet another gesture that was so alien, yet familiar. "Right now?" She repeated scathingly, "You haven't thought this through at all, have you?"

"Look, we have a plan," John said, "Well; it's sort of your plan...originally. We've got all the supplies you need to build a human body, like you said before. We keep guard on you until it's finished, then once you're back, you know, back, back. We'll destroy the – old you and head home to Atlantis."

She rolled her eyes, "I still think this is a bad idea, I told you that from the beginning, plus I'm having trouble believing that YOU were the one who came up with this."

"Well I sort of had a little help there," John mumbled under her breath, thinking of her Mrs Weir, but she ignored him.

"On the other hand it is good to know that you still have a certain level of trust for me – however faint that may be." Elizabeth ran her fingers through her hair, her expression thoughtful. "I hope you realise how long it will take?" She said suddenly, focusing back on him again, John nodded and she sighed, "fine then. Let's do this."

She set up in a large room that looked like it had originally been a dining room of some sort. The windows were boarded up and Rodney set up a force field around the entire area. Ronon was posted by the door, like a stone statue his eyes followed Elizabeth's every move, it was only because Teyla forced him to let her take over once or twice that he actually ate or slept. Elizabeth never showed any sign of being aware of his scrutiny, but occasionally John saw her glance in his direction before hurriedly looking away and returning to her work. Rodney complained incessantly of course, insisting that the city would be literally sinking without his expertise. He shut himself in the Jumper, claiming he was trying to keep up with his work load long distance, but John had a feeling he just didn't want Zelenka to take control of anything.

A team visited once a day to receive updates of their status, bring supplies as well as additional guards to take SGA-1 off duty every once in a while. Teyla returned with them once to see Kanaan and Torren, but came back the next day. Although all of the security teams were wary of Elizabeth, you couldn't disguise the faint undertone of hope that was running through them. When the news had first spread that Colonel Sheppard had found a way to bring the beloved Doctor Weir back, he'd been followed by mobs demanding to know if it was true and volunteering to help in anyway they could. And now, although everyone was wearing masks of suspicion, it seemed life had been breathed into them – life John hadn't realised had been knocked out since she'd gone.

John yawned, tapping his foot impatiently against the floor. Two hours before his shift was through and he could crash. This planet's temperature wasn't particularly uncomfortable, but after sleeping in the Jumper for nearly three days, he was beginning to feel the effects. He yawned again and then gave a start. Three days. Elizabeth had been locked in there for nearly three days. She'd said she didn't need food or rest but even so, human on the inside, she needed a break eventually.

"Hey," he turned to Ronon on sudden impulse. "I'm going to let her out, let her walk around a bit."

Ronon's eyes narrowed, "you sure? She's a machine, she can handle it."

"Yeah, but everyone needs time out sometimes."

Ronon gave the faintest roll of the eyes, "be careful, remember I'm not letting my eyes off her."

"It'll be fine," John shrugged, deactivating the force field as he walked in, gun still loaded. Elizabeth looked up, the movement so quick and sudden his eyes barely followed it.

"John, what's happened?" She asked her tone full of worry and concern. "Are we leaving?"

"No, no. I just...I just thought you might want to have a break, you know, get out a bit." He said awkwardly, looking at the floor. He really should have thought of that before, of course she wouldn't say anything herself; they were holding her prisoner here.

"Oh." Surprise was clear in her eyes, "oh, ok then. Outside?"

"Sure," he agreed easily.

It was just reaching early evening on this planet as they left, the shadows were lengthening, but the faintest rays of sunlight danced in the thick grass as they walked slowly along the outskirts of the village, Ronon in tow. Elizabeth smiled slightly as a couple of leaves drifted across her path and swirled around under their feet. She'd missed this, being able to walk in silence and enjoy the world for what it was. Stop for a minute and marvel at everything she could see and hear and feel. Pause in life and just _be. _It wasn't like she'd ever had much free time on Atlantis either but one thing she'd learned is that replicators weren't' designed to enjoy the world; they were built to destroy it. Although the rebel group had done their best to learn the human way, to meditate and watch and listen, it wasn't quite the same as being with _real _people again.

Eventually John headed towards a large tree and flopped down under it, Elizabeth hesitated for a moment and then slid down beside him. "Thank you," she said simply.

John frowned, "for what?"

She smiled slightly, "for getting me out of there."

"You still haven't killed that old habit of working yourself to death have you?" John teased.

She shot him a look, "oh well, without you to drag me away, I'm sure I would have lived in my office." Elizabeth laughed, revelling at how easily they were slipping back into their old relationship. If there had ever been a doubt in her mind about still being _her _inside, then that was gone now. It felt so natural, to be back with her old friends – her old family, even with security teams watching her every moment of the day. Not like the iron mask she'd had to force on for the last two years.

They lapsed into silence for another couple of minutes and as Elizabeth watched the sun sink down between two hills in the distance, a sense of déjà 'vu washed over her. Yes, sitting here with John, finding her old self again was so familiar, as effortless as breathing and no wonder because it was like all the other times, all those times they had escaped to the balcony to be free – just for a moment – of the stress's and the worries and the fears of ordinary life.

That's what it was like here. Like their balcony. Her and John, together, watching the world go by without them, for once not saving or helping or guiding it. Just watching.

She glanced up and John – caught off guard – grinned at her; full of the near perfect peace she knew they both felt right now. He stifled the expression at once, but, as she allowed a small smile of her own to touch her lips, Elizabeth closed her eyes and settled back, leaning against the rough bark of the tree, her face tilted up towards the alien sky.

Yes, this was exactly like their balcony.

It was almost two weeks later when it happened. John wasn't on guard at the time, but he heard Ronon's insistent yell, followed by Teyla's calling. Wheeling round he leapt out of the Jumper and ran through the thinly spread tree's towards the house, barely hearing Rodney's muffled curse as he dropped his tablet.

"What? What is it?" He gasped as he burst in the door and skidded to a halt in front of the two of them.

"Why don't you look and see for yourself?" Teyla suggested, she was perfectly calm, betraying no hint of worry, what the hell was going on?

John confused, but relieved they weren't' being attacked by any unseen force, deactivated the force field and stepped inside. As his eyes adjusted to the dim light, he caught sight of a slim figure standing in the shadows, he frowned, that couldn't be...not already...?

Hesitantly, she stepped towards him, the sunlight shining through the cracks in the windows, so her head was a perfect silhouette. "E-Elizabeth?" He asked, stuttering slightly.

Instead of Fran's tall, well-built form, with her dark hair and gentle brown eyes, it was Elizabeth who stood in front of him. Really her this time. Exactly how she was before all of this mess had happened, ripping them apart, forcing them on opposite sides of the battle field. This was how she was meant to be.

John looked her up and down, "you said you didn't expect to be done for another week." He accused but failed to keep any real anger in his voice.

"I sped the process up a bit," Elizabeth replied, "It's amazing what you can do with good motivation. John nodded still unable to believe it was really her that his plan had worked. He examined her again. How many times had he thought about her, remembered her; fought that excruciating, stabbing pain in his heart and forced himself to relieve every detail? How many times had he lain in bed and her face – though sometimes blurred among so many others – had been the last thing he saw before closing his eyes and the first thing as he woke up to face another day?

His memories hadn't done her justice. Everything about Elizabeth, everything he recalled, was here now a thousand times brighter, more vibrant, more real and more full of life than anything he could visualise in his weak memory. He took it all in, almost breathing in her old scent, while fighting to keep his face under control.

She wore the simple black pants and v-necked red T-shirt of the Atlantis uniform; he guessed it was her way of subtly reminding everyone of who she used to be; where she used to belong. The clothes clung to her petite form; he'd forgotten exactly how small and slender she was, how the strongest will he knew was disguised in this slight figure.

In contrast to Fran's tanned colouring, her skin was the perfect shade of ivory, clear and smooth and made her green eyes stand out even more; John knew he could gaze at them for hours and never see the bottom of the swirling depths. Even her hair was the same length as it was when she first got hit by the replicator beam, reaching just below her shoulders in a curling waterfall of dark brown with the slightest hint of red. It was slightly messy; even now her delicate fingers were running absentmindedly through it. She smiled slightly, and let her hands fall, shifting a little as she faced him, he stared back; wordless.

"Yes, I resisted the temptation to build myself a body to get me a place on America's Next Top Model," Elizabeth said, easing the quiet. Her voice...he'd become so used to her articulate words and sentences flowing in Fran's soft tone. Like the replicators eyes, it was so soothing, so passive. Not like Elizabeth's, her voice was one of authority, clear and strong, with that hint of steel. Yet another thing that had so easily slipped through the gaps of his sieve-like memory...

"Yeah, well...I think they call that cheating." John answered.

She laughed softly, a single clear peal echoing around the room. "Yes, as a general rule, I suppose it is." She agreed, "I doubt they've really considered that problem before though."

John gave her a crooked smile, "well, its good to have uh, you back." He frowned, "I mean you – as you you –"

She laughed again, the sound like golden wind chimes. "I think I understand. Thank you John."

He grinned at her, unable to help himself. It wasn't just because she was human now and virtually defenceless that this joy was flooding through him. They stood there for a long moment; the silence enveloping them, not uncomfortable but eventually had to be broken. "C'mon then." John muttered, gesturing towards the door.

Elizabeth nodded and – after John had scanned the room for any other remains apart from Fran's now stiff and unyielding body laid in the corner, ready for Rodney to destroy later – allowed them to leave. Suddenly she stopped, fighting down the wave of terror building up, as the realization overcame her.

This was it. She was going home. She was leaving this planet. Back to Atlantis.

In their daily walks in the fresh smelling forests and fields John had told her about everything she had missed over the last two years. She'd heard about Carson's sudden resurfacing, Woolsey's appointment as commander and their previous alliance with Todd. Listened eagerly as he retold their dramatic return to Earth and the Milky Way galaxy, about Rodney and Jennifer, Ronon and Amelia, Teyla, Kanaan and Torren.

Now those stories weren't just going to be stories anymore. They were going to flood into her life and become reality.

However there were many other aspects of reality that weren't so pleasant to imagine. The IOA and Pentagon for one, she still wasn't prepared to believe rescuing her was as easy as John made out. But she was ready to face them.

Wasn't she?

Elizabeth swallowed the panic rising. It wouldn't be easy; it never was. She knew that, she would survive. After two years with replicators how difficult could a bunch of big-headed politicians be? This was what she wanted wasn't it?

So why was she suddenly fighting off the urge to run as fast as she could and disappear into the trees and reassuring tranquillity of this alien land?

"Hey?" John said from beside her, she turned to him and forced a smile. He frowned slightly, his eyes warm and sympathetic. "Ready?" He asked softly.

And suddenly she was, Elizabeth smiled back at him, her own eyes conveying the gratitude she felt at his wordless comfort. "Let's do this." She said.


	4. Chapter 4: Welcome Home

***Refusing to make eye contact* I know! I'm sorry! It's been forever since I've updated; please forgive - my life's been hectic recently but I promise I won't bore you with that on top of all of my other sins. However rest assured for those of you still actually waiting for this story (I won't blame you if you've given up) I have not forgotten! There's plenty more to come and to make up for the guilt-deserving long gap this is a double chapter update. I promise I will be more frequent from now on.**

**So summary: John after meeting Mrs Weir has rescued Elizabeth (in FRAN form) who has rebuilt her original human body. They are now returning to Atlantis...**

**Chapter Four: Welcome Home**

"Well, she's definitely human." Jennifer announced hours later.

"I think we realised that," John said. "Tell us something we don't known doc."

"Oh, be quiet," Jennifer's irritated tone completely let down by the laughter in her face.

"Would you like her to leave that detail out?" Rodney demanded, jumping chivalrously to her defence.

John opened his mouth to retort when Elizabeth cut in. "Alright, we've established that I'm unable to beat you all up anymore." She said, shooting John and Rodney hard stares from her position, propped up on the pillows. "What else?"

"Is she really harmless?" Woolsey questioned bluntly, "what other threats does she pose?"

"Right now; none." Jennifer replied, she glanced at Elizabeth. "You're defenceless and vulnerable."

"I never thought the day would come when I'd consider that a good thing," Elizabeth commented dryly.

"Apart from that you seem to be a completely normal, average human being." Jennifer continued, "in perfect health of course, but you are identical to the old Doctor Weir, no one could possibly tell the difference."

"Sounds good." John agreed.

"There is one thing though," Jennifer began hesitantly, glancing down at her tablet again, "its not anything wrong as such, I'm just wondering," she swallowed, "when you first proposed this method, you said you were build a human body that had accelerated healing abilities, you would be less susceptible to injuries and wounds, but as I said your readings have come up normal. Is there something you missed?"

Woolsey frowned, "I do recall that was part of the agreement," he said sternly, "Doctor Weir?"

Elizabeth flexed her fingers once, nervously focusing her gaze on the bleak infirmary floor. "I – I wanted to be human again." She started slowly, raising her head to meet the four pairs of sharp eyes, "I mean fully human, as, I was... before. I wanted you to be able to trust me again, as me. I didn't want to be a replicator human, different, special, stronger." Her eyes tightened, "although that does have certain...advantages, I knew in the long run it would mean I could never be part of you again. I don't want to be invincible; I just want to be..." She stopped, a frown between her eyes, wrinkling her smooth forehead. "Its hard for any of you to understand," she sighed, "but after everything...I've been through; living – embracing life again is the most precious thing anyone could hope for – whatever the cost."

Nobody said anything for a long moment. Elizabeth twisted the corner of the blanket between her fingers; opening herself up like that had never been easy even before living with machines for two years. Expressing her feelings, emotions right then had been unavoidable but that didn't mean she was comfortable with it.

Jennifer broke the silence, "well overall, I can safely say with absolute certainty you pose no threat," she promised Woolsey calmly.

He nodded; "very well," he said stiffly, "If Doctor Keller is certain that I presume there is no reason why you shouldn't look around the city a little, you will of course need an escort –"

"No problem," John intervened, as Ronon and Teyla entered the infirmary to join the crowded bedside. "We can handle it."

"Excellent," Woolsey said, "well, if you'll excuse me I have some work to attend to," he strode out.

"He still doesn't feel completely comfortable here, does he?" Elizabeth observed quietly, staring after him.

"No." Teyla agreed in her soft voice, 'he does not."

Ronon grunted and John shrugged, "do you want to get out of here now?"

"Actually," Elizabeth said, a smile slowly growing on her face, "I'm hungry." Five perplexed faces frowned at her, "although I haven't needed to eat for two years you do miss it," she explained, "replicators don't usually enjoy food much."

"Well, I can't think of _anyone_ who actually enjoys the food served at the mess hall at the moment," Rodney grumbled, "seriously its disgusting, I mean I dread to think how much lemon they much use in all the – "

"Rodney!" Jennifer interrupted, she gave him a slight grimace, "I think she gets it." She whispered apologetically.

Rodney snorted but shut up, something only Jennifer had ever been able to make him do. Elizabeth rolled her eyes and swung off the bed, swaying lightly as she stood.

"C'mon then," John said, "lets see if you notice what's changed."

Elizabeth sat in the mess hall, listening to the wind howl and wail through Atlantis's spires. Surprisingly she actually found it hard to concentrate on the bowl of pasta in front of her; she kept stopping and gazing out of the arching windows leading out to the walkway and ocean below, far more distracting than even the most exotic of sauces the kitchen staff had concocted. Subtly she breathed deeply a couple of times, absorbing the clear air that had that unique mix of sea breeze, a delicate scent that was similar to perfumed candles and another unidentifiable smell she only ever associated with Atlantis. Even being back on Earth hadn't washed away the wild, alien odour that had clung to the city since the moment she arrived.

"Ma'am?" A voice inquired.

Her head shot up, eyes widening with surprise as she took in the two figures standing over their table. "Major Lorne! Chuck! It's good to see you again."

"You too Ma'am," Lorne replied as calm and stolid as always, "we just heard you'd returned, though Sheppard didn't exactly try to keep it quiet." He shot a look at John, sitting by her side and he gave a lazy grin back, unrepentant. "We're glad he managed to get you back after all."

Chuck laughed, "The city hasn't been the same without you Ma'am," he added. "We all missed you."

Her expression warmed, genuinely touched. "Thank you," she said softly, "that means a lot to me."

The two of them grinned and she could still read human emotions easily enough to see the honest sincerity in their expressions, "do you have time for a break?" She asked, "Take a seat."

"The boss isn't going to report us?" Lorne teased, dropping into the chair beside Amelia, who had joined them a couple of minutes before and was now absorbed talking to Ronon, Chuck joined opposite him.

"I'm sure they would –" John began,

"– if they were around," Elizabeth cut in, narrowing her eyes in warning. John shrugged looking unconcerned but there was a faint glimmer of something in his eyes; Elizabeth frowned and glanced around suspiciously.

Chuck saw her look and leaned closer, "don't even ask what else he's up to Ma'am, trust me you don't want to know." He muttered in a low voice, "You should have seen him convincing Stargate Command to get you back, half the city was terrified for days on end." He paused and gave her a wry grin, "not that it stopped them from supporting him." Elizabeth laughed lightly and was about to reply before another voice interrupted.

"Doctor Weir!" A Czech accent was more intense than usual in its excitement. "Is it really you?"

"Doctor Zelenka!" Elizabeth looked up again to see yet another familiar face.

"I havze been offworld for the last two days, since _Rodney_" he emphasized that name and gave the scientist a familiarly frustrated groan, "claimed the people on the planets erm, difficult diet was a problem for him." He shook his head and waved his hands in a gesture of despair, "You can have no idea of how glad I am to have you back. Truly there have been times when I was being driven to the very limits of my sanity!" He said tragically, collapsing into the remaining place at the end of the table.

Rodney scowled at him, "don't blame me!" He protested, waving his knife precariously and consequently dropping it on Lorne's foot; the Major winced and picked it up from under the table. "It's not my fault that you're so blatantly incompetent. I'm surprised_ I_ haven't been driven to the limits of my sanity."

Elizabeth met Teyla's amused gaze across the table and she laughed silently, wondering how her friend had managed to stand this for two years. The Athosians women's mouth quirked slightly and she gave the slightest of shrugs to her unanswered question.

"Elizabeth." She said suddenly, her voice quiet but carrying clearly through the other conversations and bickering going on either side of them. "Kanaan and Torren have just returned from New Athos, I was wondering if you would –" she stopped for a moment and then summoned up a smile, "– if you would you like to meet them?"

Elizabeth looked at her at her, studying her face. She knew how much this meant to Teyla. John had told her how protective she was of Torren; this wasn't just a polite courtesy, the smile she was wearing wasn't just a false mask to make her feel comfortable. It was the smile of old, the sweet smile of friendship that they had so often shared in those unseen, quiet moments in between the sudden panics and "problems" that so often cropped up. Elizabeth allowed the same smile to blossom on her face. "I'd love to."

"Teyla." Kanaan's eyes lit up the moment the two of them entered, "I was just putting Torren to sleep, he's very restless." The young Athosian man moved over from the decorated wooden crib in the corner of the room, gently rocking a small baby in his arms. He gazed down at Teyla, "he doesn't like sitting still much," The baby let out a yelping cry as if to further the impact of his statement, "or keeping quiet," He added.

Teyla stroked the dark hair tufting over her son's forehead, automatically moving closer to them, "I wonder where he gets that from?' She mused softly; Kanaan gave a slight grin and leaned forward, slipping an arm around Teyla's waist and drawing her close to him, gently kissing the crown of her head. The family stood in silence for a long moment, Torren's cries gradually quietening, though his eyes stayed wide and alert, watching his parents.

Elizabeth stood uncertainly by the door, not wanting to intrude on this moment. Her gaze trailed around the room, Teyla had obviously moved quarters; these were far larger than her old ones, with two bedrooms and a lot better view. She stared out the window, aware of a sharp pain building in her chest.

Torren broke the quiet a second later and started howling again, Kanaan laughed. "He definitely takes after you," he said tenderly to Teyla. He turned to Elizabeth, "Doctor Weir," he continued, "Teyla told me you were returning; there was great joy among the Athosians that day." He frowned slightly, exchanging a quick look with Teyla, "would you like to hold him?" He offered, stepping towards her, sliding Torren into her arms.

Cautiously Elizabeth took the baby, forming a natural cradle for the body; he was warm but sturdy and very soft, her nervousness vanished instantly, staring into his dark eyes, "hello," she whispered, Torren's expression was perplexed as he looked up at her, this new strange person. However he must have liked what he'd seen as with one last squawk and satisfied yawn, his eyelids dropped and drifted shut, leaning against her chest.

"He likes you," Teyla said warmly.

"He's beautiful," Elizabeth replied softly, "you must adore him."

"Yes," Teyla said simply, "we do."

"Yeah I'd say," A voice said, "he's the most spoilt baby I've ever met."

"If I recall it was not me that did the spoiling," Teyla answered, narrowing her eyes at John who slouched, lounging in the doorway. She shook her head, "that is the last time I ever let you babysit him."

"Hey, at least I'm better than Rodney," John defended himself, "I didn't drop him."

"What an achievement," Elizabeth snorted.

"Yeah well, I guess I don't have that natural woman's touch," he said, eyeing Torren asleep in her arms, "if you can bear to put him down for a minute, your old quarters have been cleared out. You reckon you can remember the way?"

Elizabeth ran her hand along the dusty surface, her fingers coming up streaked with grey powder. "No one's been here for a while," she said softly, looking around. The whole room was covered in a thin layer of dust, despite the wind and sunlight streaming through open windows. There was also had a faint feeling of emptiness and abandonment in the air, even though various photos and possessions had been scattered around, obviously collected from people on Atlantis. There was one of her old cushions on the window seat, a couple of her favourite books, a framed photo of SGA-1, her and Carson on the desk and even a crafted Athosian pot. She picked it up, tracing the patterns decorated on the outside. "You still have this then," she commented.

"Yeah well, we couldn't really send it back to Earth." John shrugged. "It was easier to leave it here,"

"So who kept it then?" Elizabeth asked. As far as she knew there weren't any security warnings against bringing clay back to Earth.

"Uh, well I didn't really want to explain about it being your birthday present and everything," John explained, "I mean, as far as I know I don't think Rodney even knows you _have _a birthday. So, um," he looked away, suddenly awkward, "I, uh, kept it in my room."

Elizabeth placed the pot back on the bedside table and gave John a hard stare, "you never did mention how you found out it was my birthday," she said casually.

"Didn't I?" John stared back, "wonder why not."

She sighed and looked away, floating over to the double doors leading out onto her small balcony with the ocean glittering hundreds of feet below.

It wasn't like the other balcony of course, 'their' balcony as she used to call it in the privacy of her mind. But it was close enough. She sighed again and her hands curling around the metal railing, John joined her.

"I've missed this," she said softly, her voice almost getting carried away by the wind.

John didn't say anything in reply but she heard the faintest of noises deep in his throat; like holding in a sneeze – or as if he was valiantly attempting to swallow a lump buried stuck in his throat.

"They all seem so happy," she went on, ignoring the reaction. "I've never seen Ronon so – full of peace, as he is with Amelia." She glanced up at him, "And I've never seen Rodney less grumpy either, what's Jennifer's secret?"

John gave a lopsided grin at that, "believe me, I wish I knew."

"And Teyla, she and Kanaan, Torren, you told me about it but..." she leaned against the arching beam. "They make such a beautiful family together."

"Yeah," John murmured, "I mean, for a while there – when she thought Kanaan and all of her people were dead, and Michael desperate to get hold of Torren – it, it..." he faded off, staring over the sea. "It was hard for her." He finished, his hands gripping the side.

"But it paid off in the end," Elizabeth said, "it was worth it." John nodded, his features softening.

"John..." She began uncertainly, and then stopped.

He put his head on one side, his expression inquiring. "What?"

She kept her eyes on the view. "Are _you_ happy?" She probed gently.

No response. Glancing sideways Elizabeth could see the faintest of creases between his eyebrows; a frown that told her exactly how uncomfortable he was with that question. His gaze suddenly flicked over to her before shying away again, but not before she'd managed to read the intense pain deep in his hazel eyes.

"Sure," he replied easily, "Life's pretty good, I suppose. I mean c'mon, shooting around the galaxy battling aliens for a living? Doesn't get much cooler than that. _And_ you get paid for it!"

Elizabeth nodded, "true." She agreed, turning away again, neither of them mentioning that he hadn't actually answered the original question.

"What about you?" John said a minute later. "Are you happy?"

"Maybe." She said simply.

John gave a half grin at her cryptic answer. Yeah, that was Elizabeth. "Well, I know it's a bit late," he said, "but – welcome home."


	5. Chapter 5: Ambush

**Chapter Five: Ambush**

Elizabeth breathed deeply as she stepped through the gate. She moved carefully down the sharply cut stone steps, behind her the gate rippled slightly as Jennifer and Teyla followed. A strong breeze blew through her long hair, causing it to sift and fly back off her face as the fresh smelling wind whirled around her.

It had been just this morning that Rodney had suggested she needed to get offworld more, get out of the city a bit, however that obvious concern for her health shattered when John asked if this sudden urge for her to go on missions with them wasn't anything to do with the ancient temple ruins written in an unknown language he couldn't quite, 'figure out'?

Elizabeth laughed quietly to herself at the memory. She'd been back in Atlantis two weeks. Two weeks of a life that had been more wonderful and full that she ever remembered. Two weeks back in the city she never dreamed she'd get to see again. Two weeks with friends that were closer and more real that she'd dared to hope.

After their reaction to her last time Elizabeth expected she would have to go through months of suspicion before they even got _close _trusting her again. She was prepared to endure guarded conversations and awkward silences from everybody on Atlantis. Expected they would – intentionally or not – ignore and avoid her, out of concern for their safety.

She couldn't have been more wrong. In her first week back she could hardly walk down a corridor without _someone _stopping to tell her how much they'd missed the old Doctor Weir and how glad they were to have her back, (some seemed to be under the misguided delusion she was taking command of the city again, Elizabeth had no clue where they could have got _that _idea from.) Even staff she hardly recognised approached and congratulated her on her miraculous resurrection.

She'd been most wary of those closest to her; those who carried the burden of command and who – no matter what their personal feelings concerning her return may be – must put the safety of the city first, no matter the cost. She wouldn't have it any other way of course, but...she couldn't pretend it wouldn't be hard.

However those fears had never materialised, obviously their fortnight stay on the other planet, the return to human form and her defeat of the final replicators had destroyed any previous concerns her team had held. After two days back in Atlantis Rodney was already bringing Ancient texts and artefacts for her to translate, eventually the paperwork piled up so high that Woolsey; (Elizabeth suspected it was out of pity and shared sympathy) found her an office. After five days Ronon and Teyla allowed her to wander the city freely without a guard. At a week Jennifer quit the daily medical check-up and just yesterday John had the guard outside her quarters taken off duty.

They accepted her again.

Admittedly there was still a long way to go, her return to Earth was being postponed daily and there was going to be a lot of icky mess when she finally did return to the SGC, the paperwork would be horrific but – she could deal with that when it came around.

"Come," Teyla said from beside her, "Let us hurry."

"I'm telling you!" Rodney insisted, "I suddenly found myself lying in some random cave, with Sheppard, Ronon and _my sister _all staring down at me. I mean seriously!"

"Rodney," Jennifer rolled her eyes indulgently, "it wasn't that bad, you're fine now."

"That's what you think," Rodney snapped, tripping on a loose stone, 'how do you know I haven't suffered some long term ill effects?"

"Well –" John began to say something but was cut off by an the air erupted in ear-splitting gun shots, a blue streak skimmed over his head and Jennifer threw herself out of the way to avoid another; landing in a pile of pine needles. There was a quick clicking sound of six guns being loaded.

"The forest!" Rodney yelled, "They're hiding in the trees!"

Teyla spun around and grabbed him; dragging him to the ground as a volley of shots shot past, within inches of them. "It is an ambush!" She dived behind a log and returned fire.

"Head to the gate!" John bellowed, also firing one handed with his P-90 into the dark wood. He shoved Elizabeth, "now!"

She didn't need telling twice; ducking the blue streaks either side of her, she sprinted towards the gate, barely a hundred metres away. Ronon was at her heels, running backwards still aiming at the figures silhouetted in the shadows.

Suddenly as they neared to the gate, five men appeared from the bush, dressed in maroon leather uniforms and holding strange, black guns, they looked large and awkward but Elizabeth wasn't going to waste time passing judgments on their firearms. Not right now anyway. One man lunged at her but Elizabeth dodged around her speed increasing as she ran on pure adrenaline. Out of the corner of her eyes she saw Rodney go down as one of the men shot him in the chest. Elizabeth gasped, a sharp stitch shooting agony through her side. She reached the DHD and rolled behind it, more shots zooming overhead, precariously close.

"Dial...the...gate..." Jennifer wheezed, crouched beside her, clutching her ankle. Elizabeth scanned her over quickly; deathly pale. They had to hurry.

Still in a protective stance bent over the DHD she punched in the first two symbols for Atlantis, surrounded by blue blurs. Suddenly without warning a hand grabbed her arms, twisting them behind her slightly. "Let me go!" She spat, attempting to wriggle away, beside her Jennifer was also imprisoned in an iron vice, another soldier gripping her in his greasy hands.

The man holding her swiftly keyed in a different address with his other hand, the wormhole activated and they began to pull the women up the stone steps towards the gate. "What are you doing?" Elizabeth demanded, still trying to rip free, Jennifer was offering no resistance, obviously bordering on the point of unconsciousness."Let us go!"

"Not likely." The man muttered. Without warning a single bullet zipped past them and ebbed itself into the man holding Jennifer, he let out an agonized yell and smashed into the steps slithering onto the paving stones with an excruciating crunch, Jennifer crumpled to the ground in a dead faint

Elizabeth's captor swore under his breath in an unknown language, "idiot," he hissed. Taking advantage of his sudden distraction Elizabeth stamped hard on his toe; he gave a furious yelp and yanked her round.

"Let her go!" A voice screamed amidst the rest of the yells and gunshots. Suddenly, out of nowhere a black shape came hurtling through the air and threw himself at the soldier, knocking them both onto the grey slabs of rock. Elizabeth kneed the man in the stomach and he finally released his hold. "Shut down the gate!" John shouted, he'd lost his gun and his only weapon were his arms; wrapped around the guards torso like bands of steel.

Elizabeth bounded off the side of the steps, landing in the dusty grass on bended knees; she whirled around and streaked towards the DHD again, taking in the others as she went. There were twelve soldiers altogether. Four had been incapacitated, including the one that had had Jennifer; Teyla was fighting two more with speed that made Elizabeth dizzy, her impromptu sparring sticks whirling and landing with echoing smacks. It was taking three men to deal with Ronon; his gun twisting and firing so fast it was impossible to see. John was wrestling with two now, rolling scarily close to the blue horizon, as he tried to claw them off him. The final man was dragging Rodney's unconscious form towards the gate.

"No!" she cried, fumbling with her P-90 and firing zinging bullets towards the guard. None of them hit him but he released Rodney and made for the gate. "Let's get out of here!" He screeched to the rest of the men, "we have one of them, leave the rest!" He lurched into the wormhole; two younger looking youths immediately obeyed him and followed.

"_Leave the rest?" _Elizabeth's mind echoed wildly, "_we have one of them? Who do they have? Not Rodney or Jennifer!" _No: they were unconscious but the soldiers were leaving them.

"Sheppard!" Ronon's throaty roar rang out, Elizabeth spun to where his gaze was directed.

"John!" She screamed, her stomach lurching, so she was almost choking with horror. The two guards holding him between them – helpless and trapped – grinned at her and backed towards the gate; she jumped towards them, fury overwhelming her being.

"Elizabeth, no!' John let out a muffled yell, before one of them struck him over the head. Blood seeped from the wound, tricking down his cheek as he was dragged through the event horizon; another two men followed before the gate shut down. Almost instantly silence fell over the group, punctured only by a final gasp of one of the soldiers as he breathed his last. Teyla stood stock still sweat pouring down her tanned shoulders and her sticks still clenched in tightly knuckled hands. Ronon spat hard on the ground, the eerie, unnatural quiet becoming deafening.

Elizabeth took one step towards the gate and faltered, breathing coming out in harsh and uneven gasps, she turned to the two of them, the horror she felt inside clearly mirrored in their eyes. "Dial the gate." She ordered, as they remained motionless, like they'd be transformed into statues. "And take the bodies back; once Jennifer comes around she can examine them. We must find him." She paused, "We _will _find him."

"What happened?" Woolsey stuttered, as the remains of the light-hearted team he sent out barely three hours ago, returned grim faced and weary. His sharp eyes scanned the two bodies clothed in Atlantis's uniform, amidst the sea of leather maroon. "Are they alright?"

Teyla nodded her eyes full of the concern that the rest of her body hid. "They were shot;" she explained, "we _presume _the guns used were only stunners but..." She bit down on her lip, worry clouding her face. Woolsey nodded, the medics already placing the two doctors on stretchers.

"Take them to the infirmary immediately," he ordered, turning to Ronon, Teyla and Elizabeth. "Where is Colonel Sheppard?" He demanded. Why was it always that man who seemed to get into all the trouble?

Almost instinctively, the other two glanced over at Elizabeth who spoke without hesitation."He was captured," She replied swiftly, her tightly pressed lips betraying her calm tone, "some soldiers managed to force him through the gate." As she spoke she began to stride up the stairs to the chaotic control room flanked by Ronon and Teyla. Richard scuttled after them, still completely confused.

"Chuck!" Elizabeth called.

"Yes Ma'am?" He looked up from behind the console.

"See if you can get a lock on this address," she ordered. "I saw one of the men dial it back on the planet," she explained, barely glancing back at the other three. "If you can, send a MALP through immediately." Scanning the room she frowned. "Ronon, Teyla, fetch Major Lorne and order him to have his team standing by as soon as possible. SGA-4 as well, we have no idea what size of force we're up against."

Teyla gave a single nod, "you are certain you have the correct address?"

Elizabeth gave a slight smile, her mouth set in a line; hard and determined. "Yes."

"We'll be quick." Ronon growled simply, before they left.

Richard stared after them for a minute, still trying to wrap his head around the proceedings. "Now – now just wait a minute –" He stuttered. Was she really giving *his* orders to *his* people as blatantly as that?

"Have some men clear away those bodies," Elizabeth ordered Amelia, "they'll have to be examined."

Well the answer was obviously yes then.

"Doctor Weir," Richard began, "Doctor Weir, can I just inquire –"

"Doctor Weir!" A technician called, "we've got a lock on the address; the MALP is going through now."

Elizabeth peered over their shoulder, "readings?"

"Atmosphere seems normal, nothing in the immediate area."

Richard attempted to follow her desperate flitting from one console to another. "Doctor Weir," he tried again, "if I may –"

"Doctor Weir!" Zelenka bounded up the stairs, his hands gesturing frantically. "What iz going on? Is it true Colonel Sheppard haz been captured offworld?"

"If I may just –"

"Yes Radek, it is," she replied calmly. "The recon teams are being assembled now." She turned back to Chuck's console.

Richard watched his mouth agape. "Excuse me," he attempted to interrupt, as the noises surrounding them began to quieten, she obviously didn't hear him, swiftly whisking around the follow the MALP's movements on camera. He moved to tap her on the shoulder, before she darted in another direction. "Can I –"

"Still nothing Ma'am," Chuck said to her, "no buildings. No energy signatures. Nothing."

"Doctor Weir?" Richard cleared his throat loudly: no one seemed to notice, still oblivious to his existence.

Elizabeth nodded to Chuck, "very well then, see if you can –"

"DOCTOR WEIR!" Woolsey shouted, his projected voice echoing around the entire gate room. Silence fell at once, a deathly quiet taking over, replacing the ear-splitting rush moments before. Every pair of eyes in the area slowly revolved to stare at him; their gazes accusing and irritated. He felt his face begin to redden as he turned and faced Elizabeth, now bent beside another scientist, "_I _am in command here," he said to her, "Please remember that before you begin to give out orders.

Her face darkened, a steely glare taking over. "I –"

"Doctor Weir!" A medic appeared in the room, their face flushed and nervous, Elizabeth turned to them, distracted instantly.

"Yes?"

Richard rolled his eyes; he may as well give up now, in the space of the last five minutes it was as if Atlantis had travelled back in time three years. Back to when Doctor Weir was in command and he was no more than an interfering busybody. It certainly felt like it.

"Well who knows?" Richard mused despairingly, "Stranger things have happened out here, for all I know we could have been catapulted back into the past." He gave a sigh and – delicately sliding them off his nose – began to polish his glasses. Right now, it didn't really matter; all he knew was that if anyone had a chance of getting the Colonel back, it was this spirited woman in front of him.

He just had to push down that fear, that maybe even Elizabeth Weir couldn't help Sheppard now.

**Hope you enjoyed! Yes I have resorted to cliffhangers :) but the next chapter should be up soon. *Trust Me*. **

**Reviews are always appreciated whether gushing, constructive criticism or flame - I just want to know! **


	6. Chapter 6: Don't Let Them See Your Fear

**Ok; not really happy with this chapter but I decided to post it anyway and will probably come back and edit later. Hope people enjoy anyway.**

**The story takes a slightly darker turn at this point as John awakens... **

**Chapter Six: Don't Let Them See Your Fear**

Something sharp and pointed jabbed at him, puncturing the thin bubble of peace and comfort surrounding, and making him all too aware of his throbbing, aching body.

"Ow," John gave a groan as his eyes sore eyes forced themselves open. "That _hurt_."

No answer came except in the form of another poke – harder now.

"Five more minutes." John was still unwillingly to wake up.

The jab this time was much more painful; piercing his side, the pressure of it forcing his eyes to flick open instantly.

"What the..._dammit_!" He disintegrated into swearing as the past events all came flooding back.

Attempting to leap up the soldier slammed into something hard and hot that sent darts of fire through his blood. He gave a yell and collapsed again.

He was trapped in a horizontal position; stretched out on his stomach, staring down into blackness.

There was hardly a difference to having his eyes open or closed; the room he was in was completely black; the dark hard and oppressive.

"You guys are keen on your colours aren't you?"

No reply.

Straining, he tried to twist around from his spread-eagled, pose but again, only encountered sizzling hot walls.

His breathing hitching slightly he attempted to kick one of his legs and gasped through clenched teeth as the fast-becoming-familiar stinging shot down his leg.

Panic beginning to rise as John tried to move his arms, his hands, his neck: All the same – his whole body felt as if fire was sizzling through its very bones.

He was being crushed, buried alive; the darkness itself was pressing down on him.

"Breathe." He told himself as an excruciating shudder ran through his body.

"Just breathe._ Think_ about this." He exhaled deeply: trying to assess the situation.

They'd be on the planet...P-4X571. They'd been examining some ruins.

Well: Rodney and Elizabeth had been examining the ruins; the other four of them had just been hanging out, flicking pine cones at the irate scientist.

Then...ambush – soldiers. He frowned, his mind picturing the men; did he recognise any of them? Their weapons? Their uniforms?

No.

The team had tried to make for the gate but hadn't been able to get there in time.

John frowned again; his forehead furrowing. All got a bit fuzzy from there, were they ok?

He guessed so; otherwise they'd be trapped here with him.

"Alright." He snapped, relieved to discover his voice at least still worked and attempting to put some sarcasm into it.

"I'm up now. Happy?"

A voice seeped through the darkness. "Not _yet_."

Ignoring the slight shudder at being talked to by disembodied voice John managed to roll his eyes. (Another part of the body that still worked).

"Well, seeing as I'm going to be stuck here for a bit while you make up your mind, why don't we introduce ourselves?"

He paused, straining his ears and eyes in desperate hope something he'd said might actually merit an answer.

"Uh, well, maybe you could turn the lights on so I can really see you and then we can get talking?"

"I can see you."

"Well, good for you." John mumbled.

"Not sure I'm all that great to look at right now but whatever." He stopped for a moment. "Seriously though, have you guys ever heard of light switches?"

There was a hiss before he was blinded by a bright flash and then the entire room was illuminated in a bluish glow.

John frowned surprised they'd actually listened; The area was small, only a couple of square metres each way, with a low ceiling, immediately making him feel claustrophobic, not helped by the black decor.

He himself was suspended in mid-air, not far off the ground, surrounded by a crisscross design of narrow, electric blue beams forming a rectangle cage around him. There were no windows, no skylights and he could barely make out to silhouette of an open, sliding door on the far wall. That was it.

Escape from this place wasn't going to be easy.

"Uh, thanks." John resisted the urge to struggle again. Even with the light on the experience of being trapped in a small space was stifling.

He swallowed fighting down unease clogging his throat. "Now, we're getting somewhere."

"Indeed we are."

His eyeballs swivelled around to see his captor.

The figure looming over him looked like the men that had captured him before and was surprisingly ordinary.

Dressed in the same maroon leather uniform, tall, straight-backed with a head of thick grey hair tied back in a tight pony tail he could pass for any stranger in street – if it wasn't for the eyes.

Like pools of swirling ash set deep into his lined face, they were pure black, even blacker than the room surrounding them, too dark to see his pupils, so he stared out at you through flat, blank irises.

Gazing back; for the first time John felt a true, unadulterated shiver of fear ripple through him.

Fear of what this man could – and would – do, without hesitation, without thought and without regret.

For the first time John realised how much danger he really could be in. How much pain really could be ahead of him: because, the eyes warned him that there would be a lot coming.

His stomach tightened and with a great effort he shoved the terror further down inside of him: burying it under a mound of anger and defiance.

"Finally." He said, cautiously craning his neck to meet his gaze.

"Nice to meet you, I'd shake your hand but as you can see your guest rooms need a bit of work."

He gave a slight grimace, allowing a confident smirk to creep onto his face. His number one rule: Don't let them see your fear.

The man continued to stare him down a smile playing around his lips.

"Lieutenant Colonel John Sheppard."

"I'd ask how you know my name but I'm guessing you're not going to tell me,"

The man raised his eyebrows. "You assume wrong." He responded silkily, "You will never leave here, so there's no harm in telling you."

He paused, the almost gleeful look on his face growing stronger. "We told all the others and they never had any hope of hurting us."

"All the – others?" John echoed nervously.

The man nodded and started to pace slowly around the dark room.

"We are a race of people called the Qaris." He began. "Although most of our population are – by all appearances – a simple people, we harbour hidden power, cloaked under our peaceful mask."

"Yeah, I used to know some other people like that." John wheezed under his breath."Weren't always good at keeping their underground hatches__shut though."

His captor took no notice. "Though we are not an advanced civilisation ourselves."

The tap, tap, tap of his boots seeming to grow ominous as he began to circle him.

"We survive by – borrowing– other races superior technology. Not with force of course." He assured him with oily smile. "We find no need for violence, but with stealth and tact rather than military strength."

"So you're scavengers."

"Some would call us that; yes." He agreed smoothly, continuing to pace in a slow, even loop.

Was it just John's imagination or was he getting closer?

"However, just recently a new rumour has begun to spread. A rumour that reports that a group of the Tau'ri have returned from a distant galaxy, returned in a flying city. A city of infinite power, resources and knowledge."

He was getting closer still –just rounding his head now.

John almost sprained his neck trying to keep following the slow, sinuous movements.

"A city that – if our various sources were correct – was originally the creation of the gate builders themselves."

He paused for a moment, towering above his head.

John could only gaze up at him, trapped and helpless, but still forcing the old mask of cocky confidence to remain in place.

"Such a city would be worth so, so, much to our people." He went on. "What we could gain from such a discovery would be..." He faded off, as if unable to finish the sentence.

John wasn't sure he wanted him to.

"Our leaders were prepared to sacrifice anything – anyone, to get their hands on such technology."

"So you ambushed us." John put in, scorn colouring his tone.

"It was simple really." He replied, unperturbed by his obvious fury.

If anything he seemed to find it uplifting.

"It just took a little arrangement, a little getting to know you're various allies and little careful strategy." He let out a hollow laugh that sent ice through John's blood.

"And now you are here." He finished slowly, eyes still boring into his face.

Behind the dark shadows John could read rising expectation – excitement – for something that was coming, something he was going to enjoy.

"Well done." John let out an awkward chuckle.

"So, what you going to do with me?"

The man ignored him, continuing to speak in the same calm, measured tone.

"John, do you know what technology my government had put a particularly great amount of effort into collecting?" He asked sociably.

"Haven't got a clue," John replied just as easily. "Sorry."

"Interrogation instruments." He emphasised each syllable clearly, "devices used for ... questioning ...prisoners."

John licked his lips, his throat dry.

"Oh." He croaked feebly, "I should have guessed. That what all this fancy equipment is for?"

He attempted to gesture to the room but had forgotten about the cage encasing him; letting out a silent gasp as his hand hit one of the blue beams.

The captor watched in amusement, one side of his mouth twisting up into a sneer as John clutched at his burning fingers.

"Oh, I do apologise." He said after a long pause. "I haven't introduced myself – how rude."

He shook his head as if in surprise; John watched him, muscles tense, eyes sharp.

"I'm Lieutenant Kaleb Rhine. Private Interrogator for First Minister Melivick of the Qaris."

Another twisted smile."As you can guess, I have done very well in this new, sudden demand for –"

"Torture." John finished abruptly, his voice hard."You make profit out of other people's pain." He snorted. "How noble."

"Oh, I wouldn't quite say that John." Kaleb replied, looking wounded. "I serve my country, they do profit from my..." He paused. "Achievements."

John coughed."Yeah, sure; you just keep telling yourself that."

Kaleb didn't reply, just laughed; looking at him indulgently; like a parent letting their child throw a tantrum knowing nobody was paying the slightest bit of attention.

"And that's why I'm here right?" John said, still determinedly casual, "you want to torture me to get to Atlantis, to steal their technology, take their power for yourself?"

"You're a smart man John Sheppard," Kaleb answered, adjusting the leather gloves clothing his hands – the gesture was so typically bad guy-ish that in any other situation John would have laughed out loud – "but let's not say I'm 'torturing' you, you're simply 'helping' us."

John snorted again, "sure, just try sugar-coating it." He managed to shake his head – though his fists were clenched at his sides. He narrowed his eyes to meet Kaleb's gaze – cool and calculating, though the anticipation was even more obvious now. "I'm not going to tell you anything." He promised, his voice coming out a dry rasp.

Kaleb simply shrugged, "we'll see." He paused, "now; let's just get you...prepared." John didn't like the way he dwindled on that word. Automatically he braced himself, he didn't care what they could do, how much they tortured him; he wasn't going to betray Atlantis– ever. They may as well kill him now, better for them; if they waited much longer this whole place was going to be taken down by army of marines coming to rescue him. His team would come; he just had to hold on.

Suddenly, without any warning at all, the cage imprisoning him vanished and with a slight gasp, John fell straight to the ground, struggling to breathe, winded by the hard marble. Before anyone could react he rolled over and leapt to his feet. Ducking under Kaleb's arm as he lunged towards him John sprinted through the door; he streaked down the dark, dingy passage outside, narrowly missing two guards stationed there. One of them grasped at him; he shook them off and aimed a kick at their shins; an agonised grunt told him he'd reached his goal. Then Kaleb was upon him again, his hands like iron vices around John's wrists, forcing his arms behind his back, "Let – go!" John spat, elbowing him in the face to enforce the comment; the Lieutenant gave an echoing roar of pain but refused to release his grip.

"Fine," John muttered, "we'll do it the hard way." Gritting his teeth he brought up his knee and jammed it into Kaleb's gut. With another furious bellow he let go of him; John was immediately tearing away from his weak grasp and shooting up the corridor towards any hope of freedom; still able to hear Kaleb's yells. "Well get him you fools!" He shrieked, anger flooding his tone. John allowed a grim grin as his pace sped up. At the very least he'd managed to cause that guy a lot of trouble.

He careered around a sharp corner and suddenly felt a sharp, aching blow, throwing him sprawling back onto the floor, staring up into the dark-skinned face of another maroon soldier. Before he could move they advanced on him, aiming a large, curved knife at his face.

Following training that had seeped so deep it was instinct; John lurched out of the way; swiftly sliding under the legs of the two previous guards who rounded the corner, taking them out by the knees as he did so. On his feet in an instant he spun around, ripping the knife from the dark-skinned guard's clenched fist and putting another three men on the ground in a matter of seconds as he fought his way through, once more racing against his captors and fate for escape.

Fate won.

John had almost reached the wide metal door at the end of the stone passage when he felt a burning pain sear across his back as a knife slashed through his thin layer of skin. He let out an agonised gasp and stumbled – the full force of the injury spreading through him – but kept running, his breath coming out in short, broken gasps. Just as he grasped desperately with shaking hands for the bolt, greasy fingers clawed forward and twining their nails in his hair, yanked him back with a vicious shout of triumph. John was flung onto the ground again, sliding along the cold stone and leaving a trail of red droplets from his wounded back as he did so.

His head slammed against the floor as he finally came to a stop, John groaned, able to taste the blood flooding through his mouth; he inched open his eyes to once again gaze up into his captors lethal face; fury twisting its features into to grotesque shapes. "You really, really shouldn't have done that," Kaleb hissed, his eyes glinting and wiping – to John's satisfaction – a glop of blood off the end of his nose. 

"Really?" John's voice was slurred, "you could have mentioned that a bit sooner?" "You know, before I attempted it." He muttered under his breath.

With a sudden movement almost too fast to watch, Kaleb leapt towards him lashing out; slamming the heel of his boot into John's stomach with savage force, pounding it into his gut so – unable to help himself – John let out an agonised yell, curling up in a ball, arms wrapped around his torso.

Kaleb drew his leg away and leered at him, "that was for before," he whispered softly leaning in close enough for John to smell his stinking breath. He nodded to the two remaining guards, limping up the corridor. "Take him back."

Once the others were gone Elizabeth didn't know what to do with herself. She paced nervously up and down the control room, stopping every ten steps to glance at the gate even though it had been barely a minute since they'd vanished through the horizon. Occasionally she'd look longingly over at Woolsey, busy in his office; at least when she'd had command in there she could always pretend to be working. Now, she didn't dare go back to private (which was nice) but isolated room high up in one of the towers; she'd have no way of knowing what was happening then.

She sighed and continued her frantic pacing, "Doctor Weir?" Her new radio gave a buzz and she started slightly, tapping her ear. "Yes?" The voice came out more urgent than she'd meant.

"I just thought you'd want to know," Doctor Wyatt's voice crackled, "Doctor McKay and Doctor Keller; they've woken up."

Elizabeth let out a small sigh of relief; at least something was going right. "I'll be right down there," she answered, "Weir out." She sped towards the stairs, forcing herself to walk at a dignified pace, "keep me posted!" She called back to Chuck, not noticing the smile spreading across his face.

"Yes Ma'am."

The two guards dragged John back up the dark passage, before flinging him back into his cell. Kaleb entered at a more sedate pace. "Put him up," he ordered, swinging what seemed to be dull gold metal baton in one hand.

John struggled while they clasped manacles to wrists and then hoisted him up, so he was hanging on taunt chains, toes barely touching the ground, his shoulders twisted. As the two guards filed out Kaleb leaned towards them, "this will be a long haul Sergeant," he said in a low voice, John appeared to turn away, while desperately straining his ears. "Make sure you increase the security detail. Double – triple the usual number of men outside that door." John gave a weary smile, the man was smart he had to admit, didn't make the same mistake twice.

"Do you think he'll be a tough one Sir?" The sergeant replied shooting John a look as he swung listlessly from side to side pretending to be unaware of the conversation.

"Oh, I've seen his type before," Kaleb said with venom, "defiant, cocky but eventually, they _crack._" He chuckled darkly and even the Sergeants echoing laugh had a quaver in it at the obvious intention in his voice.

The door swung shut behind him and Kaleb turned to John. "Now," he said, slowly stepping forward "where were we?"

"I don't know," John replied tilting his head on one side, "you tell me."

Kaleb raised his eyebrows, "we found this;" he began, taking something out of his pocket and tossing it onto the floor with a thud, "in your things. I believe I need what you call IDC's – to get through the gate." He took another step forward, "John, what is the code I need to gain access to Atlantis'?"

Johns shook his head, chuckling slightly, "you know I'm not going to tell you that," he wheezed.

Kaleb sighed, "I know," he said regretfully, "but it was worth a try," He started strolling around him in a smooth glide, still fingering the long, slender metal rod. John found his breathes were increasing in anticipation and forced them to slow.

Then he lunged. Springing forward, in a perfect, fluid movement Kaleb reached out and ripped John's shirt off at the same instant he thrust the rod into his back. Despite the pointed tip it didn't go deep but the moment the metal touched his skin it was as if a red hot poker had been plunged through him. John let out a cry of pain, writhing on the chain in futile attempts to escape, "stop!" He yelled; incoherent sentences forming as the pressure increased. "STOP!" With a quick smile Kaleb twisted the poker and pressed it deeper. Unable to stop himself John screamed at the top of his lungs, the agonised roar echoing around the small room. Agony ripped through his veins, pain, unlike anything else he'd ever felt before consuming his whole body, stabbing, stinging, aching, burning everywhere. He was hardly aware of Kaleb still standing there; the world had evaporated so he was only aware of the pain and the never-ending scream coming from his soul.

Then it was gone. John hung in the shackles panting, the faintest shadow of what he had just felt still lingering in his blood. At last he found the strength to gaze up at Kaleb; the interrogator smiled at him, gently caressing the rod in his hands. "Your resistance will only hurt yourself you know," he said, "that was the very least I can do to you; it would save yourself so much if you just gave in now. Told me what I needed to know."

Furious, John shook his head, "Over my dead body." He hissed.

Kaleb shrugged, "have it your way then – believe me; I'll enjoy it more." He smiled. "Let us begin."

With extreme gentleness he began to run the rod softly up and down John's back, making no effort to avoid the wound he'd already suffered. With the tip he would trace patterns and swirls over every piece of exposed skin, rolling it up his spin and tickling the spot between his shoulder blades. John remained silent, squeezing his eyes shut – refusing to let anything more than a gasp escape his gritted teeth, although every touch caused his whole body to shake and tremble, as if a thousand knives were stabbing him all at once.

When Kaleb seemed to get bored of this he became rougher; raking it across the back of his neck, sliding it up and down his arms and even prodding it at his face; John's eyes sprung open, a hiss released through his tightly pressed lips as the rod drove into his stomach. Kaleb grinned, noticing the reaction, and did it again, pressing the rod harder, "you didn't like that," he murmured softly; John refused to answer, his body almost going into spasm's from the pressure and his head spinning from the effort of holding the pain inside of him, Kaleb jabbed again, "DID YOU?" He roared, swinging the rod back and smashing it into his gut, "ANSWER ME!"

Unable to resist any longer John let out a scream; Kaleb tore the poker away, but just as John began to breathe out Kaleb hit again, bruising his ribs; he struck his leg, then his chest, stabbed it into the small of his back. John's screams increased as the interrogator carefully and methodically began to beat him until the pain had taken over John's body, encompassing him, possessing him, there was nothing but the agony, no thoughts, no words, no hope of fighting back or defying him; John's whole being was focused on protecting his mind from being ripped to shreds by the torture. He was barely aware where skin broke and blood began to gush down his cheeks and back.

Suddenly a gentle breath of air tickled his bare shoulder, Kaleb's seductive voice whispering in his ear. "It doesn't have to be this way John, you don't have to do this...just tell me the IDC Code John..." The metal rod was still resting lightly on his shoulder; John's vision swam before his eyes, his tongue felt thick and heavy. "Just tell me," Kaleb repeated, "go on..."

Dark hair hung over his eyes, John tried to shake it out of the way, but he had no strength. He was weak. "No..." He managed to gasp out, "I won't."

Kaleb drew away, "as you wish."

It began again.

Elizabeth scanned the concerned faces of SGA-1, Major Lorne, Zelenka and Jennifer. "We searched the whole area near the gate but came up with no life signs, no buildings, no civilisation of any kind." Teyla was saying. "It looks as if the planet is completely uninhabited; I saw no indications of farming anywhere." 

"I couldn't see any footprints or tracks either," Ronon put in, his voice deeper than usual.

Woolsey nodded, his face serious from the head of the table, "we may have to face the possibility that whoever kidnapped him travelled through more than one gate," he said, "making it virtually impossible for us to find them."

"I don't think we're quite ready to come to that conclusion yet Mr Woolsey," Elizabeth said, having seated herself to his right, "there are still a number of things we haven't tried."

Woolsey turned to her, his expression a strange mix of irritation and hopeful expectancy, "such as?"

"Doctor Zelenka was able to pull up fifty of the most recently dialled addresses from the DHD –" Elizabeth began.

"Now that may sound like a huge number," Rodney cut in, talking extremely fast, as if hoping to save time for Sheppard, "but once you take into account the address's we can't get a lock on and various other factors the amount is cut down considerably."

Elizabeth raised her eyebrows and turned back to Woolsey, "as I was about to say."

He nodded slowly, considering, "you realise though, decreased numbers notwithstanding, the amount of teams it would take to search those planets for Colonel Sheppard would drain a substantial percentage of Atlantis's resources," he asked quietly.

From the back of his throat Ronon made a slight noise that could have been a growl, "Yeah. We do." He replied, leaning forward, "have you got a problem with that?"

Lorne laid a restraining hand on the large Satedan's arm and directed his gaze at Woolsey, "Sir, every man and woman on this base is willing to take any risk to get him back," his eyes flickered to Elizabeth, "we all know what he would do to get one of us back." 

For the briefest moment Woolsey stare rested on Elizabeth too; she forced herself not to shift under his penetrating eyes. "Of that I am well aware Major," he answered, a slight smile curving his mouth upwards. He placed his hands out on the table in front of him, finger entwined and cleared his throat as if preparing to make a speech.

"Out of the many valuable and sometimes rather challenging lessons I have learnt here," he started to intone, oblivious to everyone's perplexed looks, "learnt from this from being on this city, learnt from all of you: is that you never, _never _leave your people behind, you always " he darted another look at Elizabeth, "whatever the danger. Whatever the cost." Another smile slide on to his face, "a lesson many of my colleagues from Earth might do well to learn." Zelenka coughed slightly under his breath and Rodney let out a snort, Elizabeth frowned at them although under the table her she was fidgeting impatiently. As impressive and heart-warming as Woolsey's speech was she didn't think now was quite the time to deliver it. "I have come to realize that on Atlantis, staff are like...like..." He paused for a second.

"You sound almost as if you are planning to leave us Mr Woolsey," Jennifer said, the corners of her mouth quirking.

He shrugged, firing Elizabeth yet another quick glance, "in my experience, you never quite know what is on the cards." He said. "But I would just like to –"

Suddenly his radio crackled, cutting his speech off mid sentence; gritting his teeth he answered it, "yes?"

"Mr Woolsey?" A voice came from the other end, "there's been an accident in the west hall, they're demanding immediate assistance."

Woolsey mumbled something intelligible under his breath, standing up hurriedly, "alright," He said abruptly, "I want him found. Send teams to the gates you can get a lock on."

"Also, go through the ancient data base and SGC files; see if we recognise any of the planets." Elizabeth added, rising more gracefully and allowing him to leave.

"Well," Rodney said, after he'd gone, rolling his eyes, "didn't we all just love that? He should write speeches for the president, send the whole senate to sleep."

"I believe that was just his way of showing his concern," Teyla said gently, "his feelings for Colonel Sheppard and all of us. Some people;" here she gave Rodney a hard look, "do not always find that easy."

Rodney blushed red, "fine, but I just thought he should have spent a little more time helping us get Sheppard back and a little less time practicing his skills of fine oration." He said defensively.

Elizabeth raised one eyebrow in a practiced gesture. "Yes Rodney," she said, "just like you're doing right now."

Rodney scowled at her, "oh aren't you funny," he stumped off towards the door, followed by Zelenka who nearly careered into him as the scientist stopped and swung around, "oh, and don't any of you bother to thank me when I'm the one who comes up with a plan to save Sheppard," he shot back, "you obviously have much better thing to do: like mocking me."

Elizabeth fell behind, waiting as the others all left before allowing the slight laughter on her face to fade and the full wave of pain to come crashing down on her. A whirl of terror and desperation gripping her heart in an iron hold. Why? Why was it always John? Why was it always him? Why was it always him taken or kidnapped? The rest of the team had had their fair share of unpleasant experiences but since coming to Atlantis he walked away with the prize hands down. And why now? Why when she had finally come back? After they were all finally together again? Was fate that cruel? Only allowing her to return if in exchange he...?

Elizabeth shook herself and breathed deeply, trying to come back to reality. This was ridiculous; it was _John _she was thinking about here. The trouble-maker, the magnet for accidents, the hot-headed, stubborn little boy who often seemed stuck inside the body of a responsible Colonel. He'd come home just like he always did, strutting and grinning that flyboy grin of his, while quietly offering everyone steady reassurance when _they _were the ones who should be comforting him... Yes, this was nothing out of the ordinary; he was probably used to it by now. He'd be fine, of course he would. He always was.

Elizabeth ran her hand through her hair and took another deep breath. She just had to stay in control and find him. He'd be fine.

It felt like hours later when the blood was pouring across John's back and sweat was running into his eyes and open wounds, causing them to sting and burn; that Kaleb stopped. John wasn't even aware of it at first, the pain hardly ceased anyway, but a cold blast of air revived him the shackles were unlatched and he fell to the ground, curled at his captor's feet.

Struggling up to his hands and knees John gave a hollow cough, retching up a mouthful of blood. He groaned, every bone in his body throbbing; the pain paralyzing. With a supreme effort he summoned the strength to raise his head and stare into Kaleb's eyes. "Finished?" He inquired.

Kaleb's smug expression didn't change, if anything his eyes brightened as he grasped John's neck and dragged him over to the dark wall; John pulled away, feebly trying to break the hold but Kaleb slammed him against the side, knocking the breath out of him.

John found his arms yanked behind him, elbows twisted around a pole so his shoulders were pulled back uncomfortably, the metal digging into his back; Kaleb forced another pair of manacles to his ankles and a collar around his neck, attaching it to a narrow chain set against the wall. "Oh, right," John said, "we going for the puppy look then?"

Pausing for a moment, Kaleb's lips formed the hard, bitter smile that John knew would haunt his dreams for a very, very, long time. He grasped John's jaw in one greasy hand and yanked it upwards, straining his neck. "Now listen here Sheppard," he hissed, "and listen carefully; I am going to break you. I am going to break you until the pieces can never be put back together and you are lying on the ground weeping. I am going to make sure you regret even harbouring the thought of defying me. I am going to get that code even if it kills you." Kaleb laughed, "And at this rate that looks rather likely." He moved closer as John began to choke. "I am going to get that code as you cower at my feet, begging for death." Kaleb whispered. "And then, only after I have extracted every little detail of what I need from you, will I grant your wish." He tightened his hold; John could hear a roaring sound fogging his ears.

"Now to do this I am going to use every method I know, every method I have learnt and practiced over my life," Kaleb's voice was the barest murmur now, "every instrument my country has ever built or borrowed."

"Stolen!" John corrected with a gasp, "you...stole...them..."

Kaleb snorted in amusement even as his nails gripped around John's neck. "Well, I suppose that definition in this sense is not completely inaccurate," He mused, fingering the metal rod in the other hand. "This device belonged to a late Gou'ald, to question his many prisoners or punish those slaves that failed him..." He trailed off, "I think he was one of the many your people destroyed actually," he added casually. "Funny, isn't it? The Tau'ri sought to end all torture by those "gods", never believing that one day some of the Gou'alds former power would be our greatest asset in bringing them down."

John gritted his teeth, rage blossoming at the thought, he ripped his neck away, "You won't bring them down," he croaked, his voice hoarse and cracked but strong, "you have to get through me first and I'm not going to tell you anything."

Kaleb sighed, "I've broken many men before Colonel, a number far stronger than you will ever be. Please don't think you'll be the first to escape." He tapped the metal rod against his thigh, "you have no idea what we are going to do to you Sheppard, you have no idea how much we have and will sacrifice for that city. I will not fail."

Caressing the rod gently Kaleb stepped back, heading towards the door. "Unless you have changed your mind about giving us the code," he said, "you will not be permitted to sleep tonight." He let out a short cold laugh, "that, as you will learn, is a privilege; a...reward let us say."

"You're obviously planning to keep me a while then," John commented, managing to keep his voice under control.

Kaleb shook his head, "your future does not have to be the one I control John Sheppard, it does not have to be full of the agony and death I described. It is in your hands; just tell us what we need to know and you could be free within the hour."

John had to laugh at that, "You're never going to let me go back to Atlantis now," he said, chuckling slightly, "You wouldn't let them have forewarning about your invasion."

"Perhaps," Kaleb said softly, "but anywhere is better than here. Think about it John, we could drop you off at an uninhabited planet, let you build a new life for yourself;" his voice was like velvet, "no more pain, no more torture...you'd be free."

John closed his eyes, "yeah?" His voice was hard, "and live with the fact I betrayed my people forever? Do you call that free?" He opened his eyes, battling the waves of pain and exhaustion still fighting to consume him. "You may as well kill me now Kaleb, you're never going to touch any of them."

Kaleb's eyes narrowed, "interesting..." he muttered, scanning John, "I would never have thought...but you never know...hmmm." He smiled again and straightened up, "good night John, I hope you have pleasant dreams." The door slammed shut, all light vanishing instantly.

John was alone.


	7. Chapter 7: Searching

**This chapter is pretty much just building the tension; please review especially if you have any constructive advice on how to improve my writing style ect. Thanks, hope you enjoy! **

**X-X**

**Chapter Seven: Searching **

Elizabeth rubbed her blood shot eyes and glanced at the digital clock on her desk; it was late – well early technically – she really should be heading to bed. It's not as if cataloguing these artefacts was a crucial matter at the moment, certainly not one that had to be done at half past three in the morning.

Even after all this time she still hadn't got rid of habit of working through the night.

She yawned and ruffled her messy hair; she knew that wasn't why she was still sitting here when the rest of the city was lost in a peaceful slumber. She knew that wasn't why she hadn't got full night's sleep for at least four days. She knew that wasn't why she'd refused to rest, to stop, to pause ever since John had been lost.

It had been five days.

Five days without any word or glimpse or shred of evidence that he was still alive, still out there, that there was still someone to be found. She'd got half of the team's in the city on the search, moving their way through that list of planets like it was their only lifeline. The Jumper Bay was almost empty after all the ships had been taken to scan planets for life signs.

Even the city itself felt wrong; too quiet, too hushed, too scared. Scared of what had happened to their commander, scared he wouldn't return.

Elizabeth had caught plenty of looks directed at her, plenty of whispers immediately fading as she walked past. Not looks filled with blame, suspicion and hate...the opposite...looks full of...hope.

Incredible. The people were turning to her for reassurance and leadership.

She'd virtually been their enemy for two years and, without a second thought, without a doubt, they followed her once more, leant on her, trusted her, believed in her.

Adopted her as their rock, their light, their leader.

If Woolsey noticed, he didn't comment.

However Elizabeth didn't want to think about the other whispers she'd heard, the other rumours flying around the city.

Whispers that compared the black cloud that had overcome the city since John was gone to another time...another loss.

People spoke of the time when their other leader had vanished, leaving the second one behind. Leaving him to cope with the crushing pain and grief, while still trying to lead their people to safety, trying to guard the city for her.

Elizabeth tried to ignore _those_ whispers, ignore the talk of John's and everyone else's pain and suffering back in that time. If she didn't the blame and guilt would overtake her, paralyze her, break her and she _would _let their people down.

She didn't want to dwell on it, didn't want to think about. This time would not be like the last, he would not be gone two years, he would not have to die and come back over and over. He would not have to be replaced, cast away and presumed dead. The city would not lose another leader and she would not lose him. He may have been strong enough to go through that but she wasn't.

So she stopped listening. She stopped listening to the whispers, the gossip and the rumours. She went off world at every opportunity, accompanied teams in their search for him; speaking in tongues only she knew, asking, begging for any sighting of John .

She dug her way through mission files and data banks desperately scanning for any mention of the soldiers that took him, she encouraged the team not to give up hope, not to fear the worst; that he wasn't lost, that they _would_ find him.

Tomorrow they were gating to the final planet on the list and as much as Elizabeth told herself that it wasn't the end, that if he wasn't there (and the odds weren't in their favour) they would never stop searching, never abandon him – there was still a sense of finality about it:

This was their last hope, John's last hope. That if this failed, they were trapped searching for a needle in a haystack, searching for one man who had vanished into the shadows shrouding the galaxy.

Elizabeth didn't want to face that yet.

She sighed again and closed down her laptop, not even bothering to wash out the stained coffee mug. Wearily, she slid down into bed, and flicked off the lamp, curled up in a ball under the covers.

John Sheppard never left anyone behind and neither did she.

X-X

John was left for two and half days in the darkness. Left alone for two and half days without food or water. Two and a half days huddled against the cold wall with nothing to distract but welts the covering his aching back. Two and half days forbidden to rest, prevented to sleep. Two and half days with no light or wind or noise. Just grey, bleak despair.

When Kaleb finally returned it was worse; the shackles were unlocked and John had slumped face-first onto the rock hard ground. Water had been forced down his throat making him splutter and choke. Then a lump of dry bread, was stuffed into his mouth before chains were once again attached to his wrists and he was hoisted up. Kaleb's slow pacing in front of him; casually tapping the metal rod against his thigh had only heightened John's fearful anticipation, not that he let it show.

John had remembered hearing an almost silent whistle through the still air before pain erupted in his back again; like the torture instrument had broken through the skin and slammed into his spine. Kaleb was strong, but more than that; he had deadly aim. He was able to strike John a least fifteen times with the rod, landing on the exact same spot every time. Blood flowed from the narrow streak marks across his back.

It was worse this time because John was already exhausted, stretched to the last strings of his tolerance and Kaleb was pushing harder and harder until he snapped.

It was worse because Kaleb had more time, time to experiment and discover John's weak spots – where it hurt the most, time to show off his 'techniques'.

He would take the rod in both hands, hold it horizontally and then slam it into John's ribs, throwing all his weight behind it. John was thrown into the wall behind, the stones sticking into the welts on his back, held between the cold brick and slender rod, which pressed deeper every second. Eventually with a slight pop, he'd heard one of his ribs break but Kaleb still didn't release him.

Kaleb would stand stock still for almost half an hour, swinging the rod backwards and forwards, with only the continuous crack, crack, crack, crack, crack as fire seared across John's chest until he couldn't breathe or speak, only gasp. Though maybe that was a good thing. He had vowed to refuse to cry out, to plead, to beg, to scream for release but it was so hard; he'd clenched his fists to control any sudden urge. Bit his tongue to stop any words ripping their way from his mouth but there was only so long he could hold on.

Kaleb would ask questions too – or bellow them would be the more accurate term – he would put his face right up to John's; spit dribbling from his lips as he demanded answers.

Answers about Atlantis.

There seemed to be no pattern or sequence to the questions. He'd just fire them off, demanding information about the lay-out of the city; the weaponry, the personnel numbers, the power source, the technology; blatantly hoping that John would let something, _anything_ slip, anything to help them with the eventual invasion.

John always remained silent.

When night came (or at least he assumed it was night, with no sun or way to see the time it was impossible to tell), Kaleb chained him to the wall again and warned him that the men would be watching; until he gave them the information he wasn't allowed to sleep. John didn't even reply, just slumped against the wall trembling from cold and exhaustion.

By morning, he was still conscious – but barely and bordering on insanity. There was no respite, no moment of release before he was strung up again. He was weak and vulnerable and Kaleb knew it. John couldn't summon up the energy – or the will – to defy him anymore. He had enough control to stop his fear from showing; but after just one look at that metal poker his mouth had been dry all of a sudden and his hands began to sweat at the thought of having that thing touch him again. At the very idea of feeling that pain once more.

Kaleb hadn't even said a word just, gripping the poker in one leather gloved hand, moved slowly towards him. John swallowed. He wouldn't beg, he wouldn't beg, he wouldn't beg...

He hardly remembered any of that day. Or the one after that. He could recall Kaleb aiming the poker into his gut and holding it there until he passed out from the pain. He remembered a scream escaping from his trembling lips and tears building up in his eyes although he willed them not to fall. He remembered shaking all over from pain and exhaustion, only for Kaleb to run the rod down his back once more, causing him to thrash and attempt to writher away even though he knew it was useless. He remembered Kaleb forcing him to hold the rod in his cold hands, getting him to grip tighter and tighter and then pulling away so it dropped from John's loose fingers thereby giving him another reason to punish him...

Hours –or possibly days later, Kaleb left again and at last allowed him a couple of hours sleep. Even in his hazy state John sensed he was angry – angry that John continued to defy him, continued to withhold that information that was so crucial to his people's plans. John smirked to himself, a spark of defiance still lingering; there was nothing as much fun as winding your captor up.

X-X

Elizabeth gazed around the dusty clearing that barely fit between the squat mud huts; a couple of scantily dressed children ran past, screaming at each other as they tossed a ball made of animal fur between them. Elizabeth had to remind herself that – at first glance – Teyla's people looked just as primitive as these people.

An older man with faded grey hair and creased face approached, his expression wary but with a hint of almost child-like curiosity; as he reached them he laced his fingers together and placed them to his lips in a gesture of greeting. Thinking quickly, Elizabeth mirrored the action and tilted her head, Ronon and Teyla copied her; Rodney seemed to be somewhere else completely, staring impatiently at the horizon.

"Greetings." She said her eyes not breaking contact. It had been reported that the people of this planet were very simple and isolated; from the dense forest surrounding – they hardly ever used the gate; however their dialect was very similar to Spanish, a language she could speak fluently.

"Greeting travellers," he replied, nodding to the other three hovering anxiously behind her, "I am Suolun, the Tribe Elder and leader of my people, the Lmbarii."

"I am Doctor Elizabeth Weir of the Atlan – of the Tauri." She said quickly, "these are my people, Teyla, Ronon and Doctor McKay." That was an odd slip of the tongue she admitted; she had become so used to introducing herself as an Atlantian that now...she shrugged that thought away. _Focus Elizabeth. _

Suolun nodded, old and discreet enough to pretend not to notice the slip of her tongue. "And what brings you to our humble gathering?" He asked.

"Sadly, not good...tidings." She was rusty; she hadn't spoken anything but English for two years and even then only to machines. Elizabeth cleared her throat and tried again.

"We are searching for a friend who was taken by a group of men some days ago. We were wondering if you have seen or heard anything."

He frowned, his forehead wrinkling as he thought. "What do these men look like?" He asked eventually.

Elizabeth described what little they could remember of them and how John was taken; Suolun nodded soberly, his eyes full of sympathy. "I will ask my people," he said when she finished. Turning around he began to call to the people scattered around the settlement.

"What is it? What's he saying?" Rodney demanded urgently, "look, tell them we don't have time to sit around exchanging old tribal stories about their brave caveman ancestors! We're on a clock here."

"Rodney, be quiet," Elizabeth hissed back, her brow furrowed as she tried to follow what the elder was saying. "He's asking all of his people if they've seen Sheppard or the men," she told them, "or if any of them have spotted anything unusual around the gate."

The four of them waited silently as they watched the people gather around Suolun, chattering excitedly, the words unintelligible even to Elizabeth. She breathed deeply, her heart like a lump of rock; a heavy ache in her chest. What hope was there? It was obvious John hadn't come here. Did she really expect these people to have seen him? Let alone remember the address? Even if – by some miracle – they did find the planet he was taken too, what if his captors dragged him through another gate afterwards?

Gritting her teeth, Elizabeth shoved the thoughts away, focusing back on the present; Suolun was coming back, a younger girl in tow, Elizabeth recognised her as one of the children she'd seen playing just before, maybe nine or ten.

"This is Jamiaty," Suolun introduced her, "my granddaughter."

_How nice for you. And how_ _exactly does that help us?_ Normally, meeting new cultures and people's fascinated her, (something she and Daniel Jackson had in common), however today she couldn't help but think there were a thousand other things she'd rather be doing – everyone of them leading back to finding John – than sitting here conversing with some obviously confused old man and his relatives.

Hiding her irritation, she bent down so she was at eye level with the girl, "greetings Jamiaty," she said, forcing a false smile onto her face, "it's nice to meet you. I'm Elizabeth."

"Elizabeth!" Rodney interrupted again. "What are you doing? I thought we were trying to find Sheppard, not handing out candy to children and kissing babies!"

Suolun grinned, obviously getting the gist of what Rodney was saying even of he didn't understand English, "Doctor Weir," he said quietly, his mouth quirked "please tell your friend that if he holds his tongue, we will find John Sheppard a lot more quickly."

Elizabeth shot to her feet, dust flying around. "You know where he is?"

The elder chuckled, his laugh rich and throaty, "I may not, but," he gestured to his granddaughter, staring up at them out of big, dark eyes, "she does."

Elizabeth stared at him, her mouth dry all of a sudden and not because of the dust, "how?"

"Some days ago she had been playing with her friends and they had strayed from the settlement," Suolun said, beginning to recount the story, "she had got lost in the forest and found her way to the Chap'ai to try and get home. Suddenly it activated, scaring her badly; she hid in the bushes and watched." He paused in his narrative, Elizabeth couldn't breath.

"Go on," she whispered.

"The men you described emerged, all dressed in strange coloured uniform holding unusual weapons." He continued in the same level tone, "She says they were also dragging another, different looking man with them, he seemed to be unconscious and was very pale, bleeding badly. They didn't look like traders that had come before."

Elizabeth nodded; Ronon, Teyla and even Rodney didn't say a word as the elder went on. "The leader spoke to the other men in a language she didn't recognise. They dialled the Chap'ai and when it activated the leader got out a strange device and spoke into it, as if somebody was at the other end, while the others bound the unconscious man. When he finished, they all went through the Chap'ai, taking the prisoner with them."

Elizabeth licked her lips, her fingers suddenly cold and trembling. "Did – did she see the address they went to?" Her voice was very low.

Suolun didn't say a word, just turned very slowly to where Jamiaty knelt on the ground, her eyes sparkling up at them as Elizabeth gazed at the seven gate symbols she'd drawn in the dust.

Only her carefully acquired dignity and natural cautiousness stopped Elizabeth from throwing her arms around Jamiaty in that moment and squeezing her until she couldn't breathe. As it was she swallowed and gripping hold of her composure simply replied, "She's sure this is the right address? It would be easy for her to get it wrong."

Suolun didn't say anything for a moment, just fixed his gaze on Elizabeth's, hard and penetrating; She narrowed her eyes and stared back.

"The Lmbarii are taught from a very young age to memorize tiny details and images," he said, "she will remember this address for years." He raised his eyebrows, "however your friend does not seem to have that time. You have what you need, now find him."

Elizabeth nodded, he was right; they had the address, a link, a path, a light at the end of the tunnel – against all odds they had a way to find John again.

X-X

"So, here we are again John."

John ignored him, closing his eyes. He was exhausted: one night's sleep hadn't done much to revive him and he could feel himself getting weaker.

He'd hoped that – after his captor's obvious frustration yesterday – Kaleb would be considering leaving him alone by now; going to try and find some other method to drag this information out of him. Just leave John long enough to hold on until Atlantis rescued him. He couldn't take this much longer.

However, Kaleb had swaggered into today with a new spring in his step, an edge to the sneer on his face. There was a glint in his dark eyes that told John, he _had_ discovered some new method, that there was some way he believed they could get the information they wanted.

John forced himself not to cringe as Kaleb stared down at him; probably no more than a pile of skinny rags huddled against the wall now.Ashiver ran through him, ice seeping down to his bones; the room was cold, almost freezing. They'd stripped him of everything; his P-90, his pack, snack bars, even his jacket, so he was clad in what was left of the standard black T-shirt and pants.

Where was Atlantis? His team?

It had been nearly a week now since he'd been captured (or at least John thought it was, it was almost impossible to tell in this timeless world of never-ending darkness and pain.) _We never leave people behind_. Wasn't that Atlantis's most basic code? They can't have abandoned him, can't have given up already, can't actually have _left_ him here in this hell on earth?

No. John shut that thought away. His team wouldn't give up on him; Elizabeth wouldn't give up on him. They'd come; he just had to be patient.

He'd tried to escape a couple of times but failed, never even got further than the passage outside. He'd fought and resisted and run but it was no use; there was no Ronon to help this time with his collection of knives, no Teyla to impersonate a Wraith and break him out, no Rodney to come up with some scientific miracle, not even Todd was next door to give him a hand. He was trapped. John never liked having to wait, he was a man of action of _doing, _in his experience sitting around never got you anywhere, but for once he'd just have to trust the others, have to guard Atlantis's secrets for just a little longer and then they would come. They _would._

"I have to admit," Kaleb was saying, as he attached him to the ceiling once more. "I am impressed. Never has a man resisted me for so long. You should be proud John."

John laughed, pain shooting down his battered and hoarse vocal chords at the bitter sound, "oh don't worry, I am."

Kaleb slapped him on the back, John choked back the cry of pain, "you really do have a problem with arrogance."

"Sorry," John gasped, "my...teacher used to tell me that too, I had to write out a hundred lines of 'I must not be big-headed' for detention."

Kaleb had finished and had begun to circle him as usual, "of course that makes me think." He continued, as if speaking to himself.

"You; thinking," John put it, "how unusual."

Kaleb ignored him, "you see John," he mused, "as I have told you before, no man has ever left me unbroken, no man has ever escaped, I have destroyed each and everyone of them," he paused, somehow John couldn't speak. "And what I have found," Kaleb went on, "is that the stronger the man; the greater the weakness." He turned his eyes on John, John stared back, "or more accurately, the more strong a man seems; the weaker he truly is."

For a second there was perfect silence, their eyes level, black to hazel. John was about to speak back, when Kaleb pulled away and cut in, changing the subject abruptly, "it's amazing what I hear people say when I'm...dealing with them," he said sociably. "When they're on the brink of unconsciousness and half delirious with pain. They come out with most fascinating things."

"You should be a therapist," John muttered, "hear plenty of interesting stuff then." He sighed and took a couple of deep breaths. Just as he looked away Kaleb slammed the rod into his gut, sending excruciating pain shooting up his chest, he gasped and gave an agonised roar. Kaleb rolled it a little, applying more pressure.

"Do you want to know what you told me Sheppard?" He bellowed above the sounds of John's yells, "what you screamed out that night?"

Desperately John tried to draw a breath, but couldn't manage more than brief gulps of air. "You gave me names Sheppard!" Kaleb shouted, "Names of your friends...your family I think you would call them – your family on Atlantis."

Although flames seared through his blood, John felt his heart go as cold at those words, as if it had frozen to a block of ice.

"They were hurting Sheppard!" Kaleb snarled, "They were dying and you couldn't save them! You failed!" He dragged the rod up over John's shoulder and across his neck, "You failed them Sheppard, all of them. Rodney, Ronon, Teyla, Carson and Jennifer! You failed them all!"

The rod slashed down John's back, "you begged me to save them Sheppard! You begged me to let you go in their place, because you knew you couldn't protect them, you knew you weren't good enough!"

John's scream pierced the air, ripped through the walls, as the pain –impossibly, unbearably –increased; Kaleb's voice just carried on.

"Do you know what was the last name you told me Sheppard?" He questioned, "The last name you mumbled as you lost consciousness!" He bent towards John ear, "you whispered to me to spare her Sheppard, to spare Doctor Elizabeth Weir!"

He brought the rod to a sensitive spot between John's shoulder blades and held it there; John's cries reached a new level and for the first time a tear leaked from under his closed eyelids. "Because you failed her once Sheppard! You left her behind! You abandoned her!"

Tears streamed down John's cheeks, unheard whimpers escaped from between his trembling lips. Kaleb laughed, "I was right!" He crowed, "You're weak! How did a man like you ever come to such a wonder as Atlantis? Ever get to see the sights most would dream of? Get to rub shoulders with men and women, so much more than you! You don't deserve to be around them! You'll just fail them, betray them like you betrayed her! Why would they even come to rescue you? This is the least of what you should get for what you've done!"

Kaleb whirled the rod around and slammed it against his forehead; John was shaking, unable to control himself any longer, silent pleas coming out in gasps. He could hear laughs and jeers from the guards outside; revelling in the breaking they had waited so long for. The tears just kept cascading down in a never ending flow.

"You're pathetic!" Kaleb bellowed, "A disgrace to your friends! They'll never come to get you! You only cause them more hurt! You're worthless!" He stabbed the rod into his ribcage and an answering crack accompanied John's fresh cry of pain; he hung there sobbing, sobbing as he hadn't for years.

"Just tell me Sheppard!" Kaleb ordered furiously, "tell me about Atlantis! Tell me the code! You've already failed them, already let them down! It's no use pretending anymore, if you tell me I won't hurt them, I won't hurt her! Just tell me!"

Kaleb's voice began to fade, going fuzzy as John balanced on the edge of despair, he could hardly tell whether he was in his body or outside it anymore; he tried to speak but couldn't control his tongue, tried open his eyes but they just rolled back, tried to take the weight off his aching wrists just for a second but failed.

The last thing he saw before unconsciousness effulged him was Kaleb's face, twisted in a bitter smile as he lunged towards him.

Then it was gone.

X-X

"I agree," Colonel Ellis replied, "but I still don't think you're listening to my point."

Inwardly he sighed; _politicians. _He was a military man, an officer, he commanded a war-class ship, battled with aliens and made world – galaxy changing decisions each and every day in the face of death, but dammit he could not get through a single conversation with this man without wanting to strangle him. Sure maybe Woolsey was a nice guy in reality but right now...

Let's just say it was taking every ounce of his patience not to get back on the ship he'd got off barely two hours ago and direct the Apollo back to Earth – well, Earth or a black hole; one of the two.

"Mr Woolsey!" A clear, bell-like voice broke into the conversation, the two men turned to see Elizabeth Weir coming towards them, a determined look on her face."Colonel Ellis," she said briefly, barely giving him a nod before turning to Woolsey. "We sent the MALP to the address," She told him, her tone brisk. "All readings show that the area around the gate is uninhabited, though there is some sort of enclosed settlement ahead. I have the recon team prepped and ready to go."

Colonel Ellis blinked slightly; he'd heard of Elizabeth Weir's return – that was one of the reasons he'd been ordered to Atlantis – however he'd envisioned her under guard, possibly even in a cell somewhere, not gliding around Atlantis, giving orders like she owned the place.

He frowned, "Doctor Weir, what exactly do –" As he spoke he caught Woolsey's eye, the man gave the slightest shake of his head, blatantly telling him to leave it. Ellis's frown deepened in disapproval, what was up with this place? Heaving a sigh, he shut his mouth. This wasn't finished yet.

Elizabeth appeared not to have noticed, still focused on Woolsey. "Very well," he said at last, "you leave in an hour."

"Excuse me," Ellis cut in, incredulous, all other concerns swept from his mind. "Am I hearing you right? You are actually proposing to go to an unknown world, with an unknown size force and just waltz in there and get Sheppard back?"

In a slow, direct movement Weir swivelled to face him, her green eyes sparking such fire that he almost recoiled. "Yes." She replied, her tone ominous. "I am."

Ellis was not about to let himself get intimidated by this slender slip of a woman, he drew himself up to his full height. _ "_As much as I appreciate your concern for Colonel Sheppard," he said grimly, "you must understand that we are dealing with a new and potentially powerful unknown enemy here, we must proceed with caution."

Weir's lips pressed together, if it was possible the anger in her face growing, "Colonel Ellis," her voice was deceptively soft and honey like, "we have been searching for this address for almost a week now. Today we have just acquired it and FINALLY have a way of rescuing Colonel Sheppard." She took a graceful step closer to him, somehow managing to convey the concept he was the small one here, "now are you proposing that you have just come here with absolutely *no* awareness or insight to this situation and just waltz in and tell us what we can and can't do when my people are in the hands of the enemy?"

He definitely felt that he was getting the worst of this argument and couldn't help but remember another occasion when after all his gloating and fine speeches she just turned around and threw them straight back at him destroying whatever defence he thought he had.

Ellis narrowed his eyes, "Doctor Weir, surely you would understand –"

"The only thing I understand is that you have just lost one of your best people and are sitting here not planning to do a single thing about it," she said coldly, her voice rising, "now, we have scanned the planet and calculated the risks. This is the only possible way we can get Sheppard back and unlike you, every person on this base is willing to put their own lives on the line to save somebody else!"

Ellis ignored the jibe. "But if you actually think about what you're about to do, you've got to know –"

"And the only thing I know for sure I would never do," she stood her straighter, fury literally rolling off her in waves, "is abandon one of my people in the hands of the enemy without a damn good reason. Now, I am not suggesting we walk in there without any decent plan of action, we will gate to the planet in a cloaked Jumper with a decent number of security teams. However the longer we wait around arguing over this, the less chance we have of finding Sheppard again and the higher chance we have of losing him!" Her eyes flashed and you could almost see the sparks flying from her hair. There was a long silence, nobody moved. For some reason Ellis's voice seemed to have trouble working.

"Now," she'd retained her composure once more, "Gentlemen; if you don't mind, I am going to join the recon team." She smiled sweetly at both of them, "please feel free to see us off."

And with that she was gone.


	8. Chapter 8: Remember

**Yes the next chapter is up! It's been a while and many apologies for the wait A particular note to **_**highonscifi **_**whose encouragement/nagging inspired me to get this chapter finished and published more quickly! (You'd better be reading this by the way). Chapter 9 should be up in the next couple of days riding on my sudden burst of enthusiasm. **

**Anyway: John is still being held captive and tortured while Elizabeth (after giving Ellis a serious stripping down) and the rest of the team are on their way to rescue him...**

**X-X**

**Chapter Eight: Rescue**

It was almost worse than the pain, than the torture, than the interrogation. This was abandonment – suffering in its purest form. Nightmares haunted John in that shadowy cell, nightmares you couldn't wake up from.

Phantoms from the past came and went, taunting him. The faces that mocked him every night before he slipped into unconsciousness were here, now; refusing to go, to cower away in corners where he could hide from them. Refused to stay where he could run from them. Refused to be ignored any longer. Refused to go unnoticed. Refused to become invisible.

John could only watch, helpless as figures drifted past, sometimes speaking sometimes just giving him look that said more than a thousand words. He could only watch as his mother appeared and vanished before he could reach her. Could only watch as, one by one, his old air-force comrades; those he had failed to save filed past, those civilians he hadn't got to in time, those Athosians he'd let go all passed before his eyes. Could only watch as Ford sent him a bitter glance before floating back into the shadows. Could only watch in confusion as his team and family; Rodney, Ronon, Teyla, Jennifer and Carson shuffled nearer and nearer, hate shaping their faces, could only watch as then they disappeared again, could not understand because they shouldn't be here, among the ones he had failed, because he hadn't failed them, he had saved them, they should be safe.

It was only then John realised he was staring back and forward over at his whole life, everything he had done and would do, everything he had ever achieved or failed, every moment he'd lived whether it lasted a second or an age.

His life stared back at him, laughing out of mocking eyes, laughing at what a screw up he'd made, at the pain he'd caused so, so many people.

John curled up in a ball against the wall, knees drawn up tight to his chest, arms wrapped around his legs. As he squeezed his eyes shut, trying to block out the images that surrounded him, another person glided past. Small and slim in build maybe but they seemed to fill the room with their presence just by being there. He gazed up at her, at the delicately featured face with wide set eyes lips framed by a dark fall of hair, glinting, with the slightest touch of red under some unseen light.

He choked, tears filling his eyes.

"No," he whispered, "Please, no, not her...please..." She ignored his begging, crouching down beside him, gently stroking his wet cheek with her soft fingers.

"It's alright John," she whispered softly, "we're coming to get you, you'll be ok – just hold on."

He stared at her, deep into her clear, green eyes, drinking in the colour, the beauty, seeing the truth written there, the silent promise that she would never lie, never forget, never abandon him. Then – just as he reached out a shaking hand to reach her...she was gone.

Staring at the black, empty space before him John let out a final agonised cry of pain and heart-wrenching grief. She was gone. He'd lost her again. It was over.

The final remains of his barrier broke down and John let go, he sobbed without dignity or shame. He sobbed without caring what would happen or who saw him. She was gone and for the first time in years, he truly wept.

He'd never been so alone in his life.

At that moment another thought came to him with blinding clarity.

More alone than he'd ever been in his life? No. He'd always been alone. Even at the beginning, when he'd first met her, when they'd first met, embarked out into a whole new galaxy and world of discoveries, terror, joy and pain together; even then he was a loner.

She had realised instinctively that this was someone who – despite all outward appearances – had nothing and no one. That he was someone who had been hit too hard for too long and had retreated into a place where no one could hurt him anymore. He'd tried to fit in, tried to find his place in the world. He had_ wanted _to be part of it.

But the world didn't want him. As hard as he tried, he didn't fit into any of their neat, little boxes, didn't mould to their status quo. And anyone who didn't fit didn't _deserve _to have the chance to try.

So they'd rejected him, they'd tossed him out and abandoned him; as far as the world was concerned he didn't belong. He wasn't one of them. He didn't have a place in their design he would always be the reject, the misfit, the freak, the useless, worthless piece of trash still bobbing along after the rest of the tide had floated far away.

She'd seen that, she'd known that behind the mask of laughter and strength there had been another face, filled with despair and pain. She'd wanted to help him, she _had _helped him. She believed in him. She'd seen beyond the black marks on his record and beyond his many failures and mistakes, beyond his screwed, messed up past to the future that he could still have.

She had guided him, helped him to find his place after all. Had forced him to leave the galaxy of his birth and find the home of his heart. She'd dragged him halfway across the universe to an alien city where he finally belonged.

Where _they _had belonged.

She'd given him hope, she'd given him life again, a future, friends, a family.

And she'd given him love. She'd helped him remember that he _was _human, and he_ could _love. He wasn't stone or marble or even the metallic substance of the Puddle Jumpers – he had a heart that still beat and he could _afford _to let it.

The realizations piled on with merciless speed.

He loved her. It was obvious, so blindingly clear now that John was at loss to explain how he'd never understood before.

John Sheppard loved Elizabeth Weir.

Would he ever stop reeling from the shock of it?

The hours spent in her office, the mess, the infirmary (even those bearable because of her presence). The late nights cloistered together on their balcony; darkness cloaking the inhibitions normally so controlling during daytime – hadn't he realized what they'd all _meant_? Hadn't he picked up on the signs?

John was aware _now_ of how it was Elizabeth's smile that caused a twisting sensation in his stomach stronger than any jet flight produced.

He recalled how even her briefest touch – a brush along his shoulder in silent understanding, the nudge of her foot under the meeting table – caused goose bumps to rise along his flesh.

He remembered that when two had they ruled that mythical city, ruled Atlantis – he'd take her silvery laugh above all other music in the world.

They'd been colleagues, leaders, friends and so much more: an indefinable relationship bound together by invisible bonds forged through the blood and tears shed for their people.

John had cherished her trust and friendship so preciously that it had overshadowed thoughts of any _other _feelings for her. Their partnership was far more valuable than _any _romantic connection he'd ever had and for once, he had been content with that.

But then she'd abandoned him. Betrayed him just like every other damn person in his life. Only that was wrong, because it wasn't _her, _it was _him ._No matter how much he tried to blame her, blame the replicators, blame his superiors, blame his family, it had been him along. _He'd _abandoned. _He'd _betrayed. He'd failed her.

He had let her die; let her go, let her _leave, _without as much as a fight. She returned time and time again and every single time he had failed her, he'd attempted to reach out and grab her, hold her close and never let her go, but each time he hesitated just too long, fumbled just too much and she'd slipped through his fingers once more.

It was _his _fault.

It always was.

And without her, his heart couldn't keep beating; he could still breathe, he could still live; blood still ran in his veins and oxygen still stayed in his lungs, but his heart – his heart was dead again. He could still laugh, still run, still fight but it wasn't the same. She'd given him love and without her, that was gone.

Without her, he was alone again. He was still in the place he thought he fitted, still with the people he thought he belonged with, but he was alone.

Maybe that was the way it was meant to be. Maybe some people were never destined to be part of others. Maybe his fate was meant to be a selfless one, (or appear to be anyway). Maybe he was born to protect, to fight, to defend but never to belong. Never belong.

Not without her.

X-X

Rodney glanced down at the small hand held tablet in his hand, "Can you detect anything?" Elizabeth asked from the seat behind.

He shook his head, "no," his voice was sober. He was still wondering if bringing Elizabeth along was a good idea; she was a civilian after all. (Yes, admittedly he was too but, he was Rodney McKay.) True, since she had returned to Atlantis she'd learnt how to use a P-90 and even started taking sparring lessons with Teyla but even so...he just didn't want to think about what could happen if things went _wrong._

There wasn't any point thinking about it anyway, even the slightest protest would have been useless. She wanted to find Sheppard as much as they did and wouldn't let anyone get in her way.

A couple of tense minutes passed, no one said a word; at last Rodney sighed, his shoulders slumped in defeat, "this planet seems completely uninhabited," he called back flatly, "no life signs or energy readings anywhere."

"Well we cannot just –"

"Wait! Wait!" Rodney tapped the tablet frantically; no one was stupid enough to interrupt him.

"Ok," he announced after a tense moment, "I'm getting high energy readings from a small area about ten miles, _that _way." He waved his hand in some vague direction; the pilot rolled his eyes, steering the Jumper round.

Rodney bent his head, still focused on the tablet, trying to ignore the anxiety filling the silent air in the Jumper, gnawing in his stomach like a wolf. They all knew that they were running out of time.

X-X

Teyla frowned as she peered down the large dark hole, now minus a rather worse for wear iron grate. The Earth people did seem rather fond of C-4.

"You're sure this is it Rodney?" Elizabeth was asking, "Not a rabbit burrow or something?"

Rodney rolled his eyes irritably, "oh, very funny." He rubbed his hands together and clambered over, "now;" he said peering down, "From the location of the unusual energy readings I'm presuming this is just a back entry to wherever Sheppard is being kept down there," he paused, "so there shouldn't be a bunch of big, scary men with big scary guns waiting for us at the bottom, but, uh; just in case,"

He looked hopefully at Ronon. "Maybe – you should go first?" The Satedan gave him a dark look and climbed in. Teyla smiled for the briefest second and then the reason they were there came rushing back to her and it faded once more.

X-X

Elizabeth gripped the small staples jammed into the wall as she felt her way down, the wall wasn't earth or rock or stone as she'd thought but metal; smooth and slippery. Craning her neck, she squinted past Lieutenant Mays coming down after her – at the faint square of light looming far above. She could swear it wasn't getting any further away. As she stretched her leg down again, her foot encountered a hard, flat surface, with a sigh of relief she pushed away from the wall and landed on the balls of her feet beside Teyla. 

"Where are we?"

"I do not know," her friend replied soberly, shining the torch up and down the dark corridor, the metallic wall glinting. "I cannot see anyone."

Following Ronon's looming figure they tiptoed along, Elizabeth gripped the P-90 in her cold fingers – it felt awkward – uncomfortable, she didn't know how to use a gun, she'd always hated guns (understatement) – but after Atlantis, after the Replicators she was never going to allow herself to be defenceless again.

Just as they arrived at a fork, suddenly, without warning three guards leapt out from behind a sharp corner, aiming their guns; eyes menacing. "Put down your weapons!" A blonde man bellowed; furiously, his gaze darting everywhere. No one moved. "Now!" He tightened his grip, "I'm warning you..."

There was a flash of blinding light as the blue zap from his gun smashed mid-air into Ronon's red streak, Elizabeth ducked as Major Lorne and Lieutenant Mays fired at the other two men, bullets bouncing off the walls. Within seconds the three guards were down.

"They'll have heard that," Lorne said grimly, glancing up the corridor, "They'll have been warned we've arrived; we have to hurry." He glanced at the two passages, "split up, half left, half right."

Elizabeth sprinted left after Ronon and Teyla, her heart pounding; they were almost there, she was certain.

The passage widened and round lights began to appear, studded high in the wall, gradually doors began to appear, they checked every room – almost all of them containing a strange hodgepodge of technology, that Rodney was sure was stolen.

"We should have found him by now," Rodney said, from behind her, his voice betraying the anxiety he was feeling, "We've been going for ages. Maybe Sheppard isn't here after all, I mean seriously, we have no proof, no evidence, how do we even know this is the right place? That he ever even came to this planet?" His voice was high and shrill, bouncing off the metal walls.

Ronon swung round, his dark eyes flashing, fists clenched at his sides, "he's here," he snarled, towering over the scientist, "and if you were just quiet for one minute we might actually be able to find him." He leaned closer, his shoulders heaving, "So shut it or we'll all be going the same way as Sheppard!" Rodney nodded mutely, unable to say a word. Elizabeth and Teyla glanced at each other, the same worry reflected in each others eyes. Ronon gave a nod and turned again, stomping back up the passage. Suddenly, out of nowhere, a blue streak shot past his head, missing him by an inch; he threw himself on the ground and in a blur of motion had rolled over to the side by the wall and whipped out his hand gun, spinning it round his fingers and firing at the distant figures sheltered around the far corner. Following suit Elizabeth dived behind him, her P-90 vibrating under her grip, the sound of bullets deafening her.

Rodney huddled against the opposite wall, his hands trembling but his face set; aiming at the men, distinctly maroon coloured. Elizabeth felt a hand grip the back of her jacket and whirled around in panic, however it was only Teyla, hunched in a ready crouch. "Elizabeth, they can hold them back without us!" She hissed, her voice barely distinguishable amidst the noise, "we must find Colonel Sheppard, come on!" Elizabeth nodded and the followed her friend and two other marines, sprinting a few metres up the wide passage way and ducking into corridor off the side. She could hear the few marines behind her and then further back; heavy footfalls of the soldiers, running after them. Her breaths increased as she tore through endless room, her eyes desperately roaming – scanning – for any signs of John.

"Can – can you, see him?" She panted to Teyla, just ahead of her,

Teyla shook her head, throwing herself around a tight bend and firing a few shots back, Elizabeth heard two distinct thuds as their pursuers hit the ground with booming force. She was barely aware of anything else but her laboured breath and steady beat of her feet as they ran on. Tossing her hair out of her eyes, Elizabeth's gaze widened as she saw where they were heading; right towards four hulking guards, all crowded around a large door at the end of the passage as if they're lives depended on it. Before she could even open her mouth to say a word, Teyla had casually shot the four of them down without breaking into sweat. Elizabeth couldn't even find the energy to raise her eyebrows as they burst through the entrance.

A whole hoard of guards faced them, filling up the long, wide room with yet more doors leading off it. Elizabeth skidded to a halt, for the barest, hundredth of a second no one breathed. No one moved a single inch.

Then pure chaos let loose. With a wild roar the men began to charge forward, faces wild. Teyla and the four Marines fired as they approached, bullets flying everywhere. The door behind, burst open again and Elizabeth spun around, her heart in her throat, expecting to see more guards dashing in. She raised her gun.

"Elizabeth!" Rodney cried, almost falling through the door, Ronon gave him a rough shove from behind, "have you found Sheppard?"

She couldn't manage more than a quick shake of her head before the wall behind her erupted in an explosion of marble and iron, Elizabeth dodged out of the way, running along the side of the bloody battlefield that had taken over the wide hallway, frantically trying every door that was left still standing. Out of the corner of her eye, she could see Major Lorne and his team break in a different entrance and immediately enter the fray. Gritting her teeth Elizabeth ducked under a stream of bullets streaking overhead and reached the end of the room. Gripping the gun tightly, her hands sweaty, she fired at the bland metal door, her beating heart only a reminder that it could be the countdown to how long John –how long any of them – had left.

She kicked her way through the remains of the door, her eyes taking in the dark room. "John!" She screamed, above the noise "John? Please answer me!" She scanned the shadows again; hope fading as she turned away.

"Elizabeth..." The faintest sound whispered across the room, she whirled around, breaths coming out ragged.

"John." She was across the room in an instant. She dropped the gun and crouched down beside him. "Oh my –" Elizabeth couldn't finish; her eyes filling with tears that slowly trickled down her cheeks. She forgot the sounds outside, the screams and the shouts of death, the cries of her people; she could only gaze at what was left of the man she used to know.

John was little more than a pile of bones curled against the wall; his pale skin was taunt, stretched across prominent cheek bones, giving his face a gaunt, haunted look and Elizabeth could see his ribcage through his ripped T-shirt. Blood seeped from various wounds slashed across his back, arms, legs and face and underneath she could make out bruises in various stages covering what exposed skin was left. A metal collar was attached around his wasted neck, so he was shackled to the cold wall by a thin chain. Elizabeth didn't trust her voice; she cupped his battered cheek in one hand, gently running her fingers along a gash under his bruised eyes with the other. "What did they do to you?" She whispered at last, the words cracking at the end. "Who did this?"

John's breathing was heavy and he gazed at her out of frantic, terrified eyes, feebly trying to pull away from her soft grip. Pain tore at Elizabeth's heart. "What wrong?" She murmured, "John, please... tell me."

He let out a gasp, "Elizabeth..." His voice was hoarse and rough, so low she almost couldn't hear it; she lent closer, "Go...now. You –" He let out a sharp cry, convulsing, sweat pouring down his face. She felt his hand grip hers in an iron vice, clutching at her fingers. "Go!" He gasped, "You – can't – be – here." He began to tremble.

Elizabeth stroked his forehead, worry twisting like a knife, "its ok," she soothed him; "we'll get you out of here John."

"No...Please..." He whimpered brokenly. "Not her. Please."

"Aw, now isn't this sweet," a voice came from behind them, "the little damsel in distress has come to save her brave hero."

Elizabeth whipped around, springing to her feet. A tall grey haired man was coming sauntering towards them. She'd missed him, hiding in the shadows. As he approached she looked up and barely stifled a gasp.

His eyes: Black. Flat. Hard. Empty. Elizabeth wasn't sure if she'd seen anything so terrifying in her entire life. (And that included the Wraith and Replicators.) She gulped and gritted her teeth, meeting his cruel gaze with a defiant one of her own. "And you are?" She demanded, raising one delicate brow, her hands clasped loosely in behind her in a relaxed pose to hide the nails digging into her palm.

The man saw her assessment and grinned in amusement, as if to admit he was impressed with her reaction.

"How funny," he said casually, "both of you ask the exact same questions. Even act the same way too, at first anyway." He gave her another smile, the kind your best friend gives you when you're in on a secret only the two of you know about. Elizabeth didn't reply, she didn't want to know what the 'at first' meant.

"Of course, I know who you are," the man continued, coming slowly towards her, "Doctor Elizabeth Weir. John talks you about you an awful lot."

Elizabeth held her head high, straitening her spine. "I'd explain who you are quickly," she said, her voice high and cold, "because in approximately one minute, five of my people are going to come storming through what's left of that door and then whatever you were planning will be over."

The man laughed again and she could barely suppress a shiver, "I'm sorry," he chuckled, still inching towards her, "you just have to understand how amusing this all is to me; the two of you are just so predictable."

Elizabeth balled her hands into fists behind her back, why had she put her gun down? Was she a complete idiot? She'd never felt the need to arm herself with a gun before but right now she felt as if she would give almost anything to have one in her hands. This man was probably going to kill her and John as well for that stupid mistake. Well, if she was going to die she may as well go out the way she'd always believed in. Unarmed but dignified.

She just wished John had had a bit longer.

Suddenly she felt a slight pressure pushing at her hands, a hard, unwieldy, stiff something. It was the P-90. Slowly, still behind her back so that the man couldn't see, she took a firm grip of it, pulling it from John, her fingers icy.

"Oh well," the man was saying, sighing slightly, "predictable maybe but I have to admit; your white knight here gave me a _lot _of entertainment." He leered at her, laughing "pity it had to end so soon, really though we were finally getting somewhere. He was a hard one to crack, held on right to the very end."

His hand began to reach for the gun at his belt.

In one swift movement Elizabeth had grasped the P-90 and whirled it around. "Don't. Move." She hissed.

The man froze. "You won't." He whispered.

Elizabeth narrowed her eyes, "won't I?"

The edge of his mouth pulled up in a sneer, "you forget I know all about you," he said, "I wasn't bluffing when I said John said a lot. You're a diplomat, a civilian, a person of peace."

"I was also a prisoner of the most inhuman machines in the galaxy for two years," Elizabeth countered, "that causes people to change."

He shook his head, "No. John knew you hadn't changed that much and I can tell. You cannot kill."

Elizabeth's eyes bore into his, her hands shaking – she hoped he wouldn't notice. The man grinned at her, "go on then," he hissed, "do it."

Elizabeth couldn't breathe, would she do it? Could she do it? It was one thing to fight your way through a group of soldiers firing at you, another thing to destroy a creature that was no more than a machine but to kill someone in practically cold blood...

The man was right; she was no soldier, all her life she had preached of peace and non-violence. Of finding another solution to the killing and the pain. She couldn't do this. The replicators can't have changed her that much; she was still the same person, she couldn't lose herself now, after finally returning to the life she thought she'd lost forever.

Even as she raised the gun to aim at his head Elizabeth hesitated. She couldn't do this.

That moment of hesitation meant everything. Even quicker that she had, the man grasped at his hand gun and pulled it from his belt, pointing it at John.

Elizabeth reacted with instinct. The echo of the single bullet flying from her P-90 echoed hauntingly around the small room, as did the agonised scream that escaped the mans lips as he fell to the ground, blood flowing freely.

Elizabeth lowered the gun, staring transfixed at him. The man stared up at her, his eyes full of hate. "You missed." He hissed furiously, mouth twisted in a ugly sneer as he clutched his injured arm, "did you really think you could get rid of me that easily." He was laughing, even as he winced in pain. "Oh Elizabeth, my wrist will heal."

Elizabeth raised her eyebrows, "I didn't miss." She said simply.

For the briefest second s look of puzzlement crossed his face before he masked it again. She smiled in reply. "Oh, don't worry," she reassured him, her tone hard, "you were right about one thing; I don't kill." Leaving him to crawl towards the door, Elizabeth turned to John.

"Its ok," she whispered as he looked at her, his gaze blurred with pain, "we're here John." He nodded groggily, barely conscious. She stroked his dark hair, even messier than usual. "You're going to be fine." She murmured. "We'll be back to Atlantis soon." He gave a wracking cough, eyelids slowly sliding shut in contentment. Suddenly they sprang open again, utter panic filling the depths.

"No!" He let out a roar, struggling against her ministrations, "Elizabeth – No!" She let out a gasp as he yanked away, throwing himself across the hard floor, just as a blinding blue streak shot across the room, grazing the side of his chest, so he fell to the ground with a dead thump, the chain dragging behind him.

"No!" Elizabeth let out a cry of horror, her mind unable to comprehend what she'd just seen. Her gaze darted to the door, just able to see a dark figure, still clutching a bleeding arm dart away. She gulped and crawled over to where John lay.

"John?" Her voice was the barest thread, "John, can you hear me? Please, John?" She laid her palm against his cheek, "John?" Her fumbling fingers moved to his neck, feeling for his pulse. It had to be there. It had. He couldn't be...

No. It was alright. She could feel his pulse. Very faint but still there. Elizabeth almost cried with relief, running her hands over his bruised face. He was fine – for now.

She realised that a sudden silence had fallen outside, her breath hitched as she strained her ears, trying not to make a sound.

"Elizabeth?" It was Rodney's voice, uncertain and wary as he scrambled through her hastily made entrance. "Are – are you ok? Have you found Sheppard?" Elizabeth closed her eyes for a moment, allowing thankfulness to seep through her body.

"Yes," she called when her voice was strong enough, "he's right here." She scrambled to her feet, "but we have to get him back to Atlantis – quickly. We may not have much time."

**Hope you enjoyed; although I wasn't keen on some of the more icky violence and torture in the earlier chapters I felt it was an important tool in building for John's emotional catalyst there.**

**Also sorry for those of you who were disappointed Elizabeth didn't kill Kaleb; I planned for her to right until the end and then just realised it would totally destroy the character. I'm not a super non-violence fanatic but I think it would be sad if she became a killer when her vision for peace was always such a strong aspect of her personality. So that choice was important (if annoying) and believe me I hate the guy as much as anyone else. **

**As always please **_**review**_**, constructive criticism would be especially great.**


	9. Chapter 9: Hoping

**Alright, this is an...interesting chapter; very little happens but on the other hand A LOT happens. Contradiction? Maybe. Anyway: read on! **

**X-X**

**Chapter Nine: Hoping **

Jennifer felt her stomach flip as Colonel Sheppard was carried out of the Jumper; she'd seen plenty of injuries in her time, no one could accuse her of being squeamish but she had to admit this was pretty bad. "Put him on a bed," she ordered keeping her voice level, "Now!" She glanced of the rest of his team's faces; Rodney – she could read his expression like a book; he was worried, on the verge of panic, his mouth pulled down at the corners, hands twisted together. Teyla – calm; but the skin on her smooth forehead was creased in fear. Ronon – serious, sober, almost bordering on grumpiness, though she could tell by the grim set of his jaw, the anger behind the gruff expression. Jennifer's gaze finally rested on Elizabeth; her features were relaxed, her movements quick and sure but not panicked, her emotions seemingly under control, she'd had more practice masking her feelings than the others. However when you stared into her green eyes Jennifer could see she was more nervous, terrified and full of fury than all of the others put together. She shook herself and pulled her mind back to the mind at hand.

"Get him to the infirmary," she said frantically, scanning John's face, "quickly!

X-X

To the background of harried shouts and curt orders drifting through the sealed doors, Ronon sat outside the infirmary, staring resolutely at his hand gun as he spun it round and round his hand, gaze not wavering as he followed it whirling movements. Now if he could just keep his mind as occupied as his eyes then maybe he could forget about the man trapped inside the infirmary. His teammate; his comrade; his friend...his brother.

Jennifer emerged from the surgery, rubbing her hands against her furrowed forehead, her face flushed. Rodney sprang to his feet, followed by Teyla. "How is he?" He asked immediately, voice shrill.

Ronon felt his heart sink as he took in Jennifer's defeated expression. Even before she said anything, he knew the news wasn't good. She tried to smile as she glanced up at Rodney, "I don't know," She admitted wearily, "his condition had stabilised and we've managed to clean up the wounds as best we could, but..." Jennifer's voice cracked and she breathed deeply, regaining control.

"He's simply sustained too many injuries to know for sure," she said, speaking quickly, as if to get it over with as fast as possible. "The gun shot grazed the side of his chest – just managing to miss his heart but punctured a lung, so he has trouble breathing and has obviously lost a lot of blood..." Jennifer swallowed, unable or unwilling to finish her sentence.

"And of course none of this is even taking into the number of other injuries he suffered while being held prisoner." She continued, "you said the device...used on him was of Gou'ald design," she looked at Rodney, "but we have no way of knowing what the long term effects could be; it seems to have caused mostly flesh wounds but several of his ribs are cracked, there are deep gashes all across his back, his ankle has suffered very bad bruising. Eventually someone's body just can't take that sort of abuse, it just begins to close down and then..." She cleared her throat, her tone barely a whisper, "it all comes down to tonight truthfully; if he can pull through this we can support him enough for a long term recovery, his body will begin to heal, if not...She trailed off, her lips trembling.

Wordlessly, Rodney took one of her hands in his, and slipped his other arm around her; she buried her face in his chest, squeezing tight. Teyla sunk back into one of the infirmary chairs, sagging against the wall. Elizabeth sat tall and straight backed her face pale and set. Ronon frowned fiercely at the floor, a low growl escaping from his throat. It was no use; they all got it, the message was clear – all they could do was wait. Wait to see if John Sheppard would make it through the night or slip away from them forever. Wait to see if in the morning their leader would still be lying there or if all that would be left was an empty shell. Nothing they could say, nothing they could do.

Just wait.

X-X

That night was something Elizabeth never forgot. The small room tucked off to the side of the infirmary, became a prison for all of them, a cage with invisible bars, a...torture chamber. She cringed internally at the name, a constant reminder of exactly what John had gone through. They still had no idea what had really happened in that place and right now, she might never find out.

No one mentioned the fact that anyone of them could leave at any time; that staying there really wasn't going to have any logical, scientific effect on John. They all felt – like she did – that no matter what happened tonight, they had to be to see it, stand by him, whether as a farewell party or to welcome him back.

The hours wore on; at first Rodney just ate; working his way through endless snack bars and coffee he'd lugged up from the Mess Hall, occasionally sharing some with Jennifer, beside him, between her jumping up every hour to check John's status. Eventually though, the food ran out and he became still, the two of them clasped together in silent comfort.

Ronon paced, backwards and forward, round and round, up and down, the relentless tapping soon becoming as irritating as Rodney's crunching bites and crumpling of wrappers, but Elizabeth couldn't summon up the will to tell them to shut it. Thankfully Amelia arrived and was actually able to get him to sit down, soothing him in a soft voice until Elizabeth was sure he'd dropped off to sleep.

Teyla seated herself cross legged on the ground, as if she was trying to meditate, however her eyes remained wide and open, her hands clenched fists in her lap, only relaxing when Kanaan arrived, Torren in tow. Without hesitation, he sat down beside her, softly placing Torren in her lap. Out of the corner of her eye Elizabeth watched as Teyla arms held her child against her chest, leaning into Kanaan's embrace.

A wave of loneliness rippled through Elizabeth as she looked around the room, getting for the first time a concept of how is must have been for John all this time; awkward and alone, while all of the others moved on and found a piece of happiness for themselves; their place in the world, leaving him like an pointless puzzle shape that didn't quite fit in anymore. She was sure he could have found someone if he wanted, there were plenty of women who wouldn't say no to his charm and dare-devil allure but somehow under his flyboy mask, she could read something more...an intense yearning that went deeper than he ever showed.

Someone else tiptoed into the room, quiet and unnoticed, no one looked up and he didn't make eyes contact just slipped onto the chair in the corner, staring at the floor, not saying a word. Elizabeth smiled softly at his balding head. Atlantis had changed Woolsey as well.

It wasn't just the pain and grief that tormented her that night; doubts plagued her mind. Should she have killed the man? That possible murderer?

Kaleb had been captured and literally as she thought shipped back to Earth with a prisoner of war kind of status, possibly to be used in negotiations with his government – best to get _that _threat out of the way as quickly as possible – but something within Elizabeth seethed for more than mere _imprisonment._ Shouldn't she have changed the angle of the gun just a tiny bit so the tiny bullet was fatal? Should she have murdered him, halted his beating heart and ended his no doubt, cruel, vengeful life?

More importantly is she had, would they all be here now, waiting to see if John would live through the light? Elizabeth choked, gulping, swallowing back tears that threatened to stream down her cheeks. She couldn't take this.

Without saying a word she got up, scraping the chair on the hard tile floor and strode out of the room. Slipped through the silent infirmary, past the only occupied bed, fighting back more tears as she averted her eyes from the sight of the patient lying there. Outside in the corridor she stumbled along, eyes blinded my unshed tears, unable to see where she was going just seeking to escape the pain and guilt consuming her being.

Despite her lack of direction, somehow Elizabeth wasn't surprised when her feet (obviously more controlled than her mind at the moment) brought her to the balcony. "Their" balcony. As the twin doors finally slid smoothly shut with a resolute click, Elizabeth let go; clenching the railing in white-knuckled fists she hunched up against the cold, bitter wind whistling through the twilit balcony and let the tears pour silently down her cheeks.

Was it her fault? If John died tonight was she to blame? "What have I done?" She whispered to herself, staring unseeing out at the sparkling, breath-taking view before her. "What have I done?"

She could claim to be as peace-loving as she liked, refusing to kill a dangerous man but had she in fact killed in a different way? Caused the death of another man? Only this one was one of her greatest friend, part of her family, her life and the other was an enemy.

Letting out a silent cry she wrapped her arms around herself and tilted her gaze up to the sky, the brief, shameful proof of her sudden break down still wet on her cheeks. The stars shone above her, the bright lanterns of light against the dark backdrop.

_Like life._ Elizabeth thought dully_, you fight you're way through all the darkness, all the pain and for what? For this? To watch everyone you care about get ripped away from you? Why? What's the point anymore?_

She gulped back more tears, holding them in, knowing that if she truly opened released they could keep flowing forever, so instead she looked up at the stars again; they gleamed back at her, winking softly in reassurance, She rubbed her eyes wearily, smiling a little, somehow comforted by the sight of those sparkling diamonds hanging above her; they'd be there for millions of years, solid and unchanging while the Earth turned and time itself passed; and they would stay there, guarding the mysteries of the universe for millions more.

How could she, who had had such a rare privilege of having seen the tiniest part of those mysteries, have just a few of those uncountable secrets revealed to her, berate them? She'd seen things most people couldn't even dream of and nothing could ever make her choose to take a different path, no matter what she'd been or would go through she could never regret all of this, these living miracles; she'd made that choice when she gave herself up to the Replicators.

More than that, so much more than all of that, Elizabeth knew without a doubt that John felt that way too. Whenever anything got too hard, too much take, when she felt like packing it in and fleeing to some remote corner of the Earth, he would be there, reminding her – often without words – that it _was _worth it, that what they were part of was something bigger, something more incredible that they could even begin to conceive, that she couldn't give up, that she couldn't even think about leaving.

And it worked. Every time.

Elizabeth breathed deeply and pushed away from the railing; slowly backing off until she could feel the cold, solid wall of the tower behind her, she leant against it, hands flat, her back pressed right up, slowly letting her legs buckle as she folded down onto the floor, hugging her knees to her chest, eyes still fixed on the sky, curled up in a ball.

Elizabeth remembered a night walk she'd gone on, years before when she was only eleven, with her mum and dad. It had been on a holiday in England to observe night owls habits or something like that, she'd never really been bothered about them but her parents were fascinated and she and her four brothers had been dragged along.

To the rest of the tour's disappointment they'd never actually seen any owls and Elizabeth stumbling along half a sleep in the dark, wishing with all her heart that she'd brought a flask of hot chocolate or even better – a pillow, had hardly been able to contain her sigh of relief as the guide announced they'd have to give up. However before he'd taken them back, they'd stopped off in a small clearing at the top of a hill. Elizabeth remembered the sky had been as perfectly clear, not a single cloud to be seen.

Elizabeth remembered the guide seeing her stare up in awe at the sparkling nights sky and giving a small smile and nod of approval before starting to talk. He talked of myths and legends etched in time itself some. He described stories and people and lives long gone, never to return but that still hung there, remembered to this day. He showed them the constellations and the exquisite masterpieces drawn in the sky above, there for all to revel in. He talked of what could and might be out there, of the marvels and the mysteries that so few ever though to discover.

And then it had been Elizabeth who had begun to talk, to ask, to question, demanding answers, and it had been the rest of the tour that had yawned and sleepily checked their watches, while she explored this new world that had miraculously opened up before her. The brief half an hour they spent there could hardly be expected to satisfy such, intense sudden curiosity and hunger for knowledge, so; when her twelfth birthday came around her parents had got her a telescope; so she could explore the universe herself.

Of course, like so many childhood phases it had come and gone, but from that day a yearning, a longing, a craving had been planted in her heart, a silent promise to herself that one day she would truly discover the mysteries of the universe.

Now Elizabeth looked back at the constellations, greeting them like old friends coming back to her after so long, they were different of course, this wasn't Earth even if it was in the right galaxy but they were good enough.

Elizabeth's eyes roamed over the dark sky, automatically tracing patterns, forming pictures with the stars, she was sure she was imagining it but one certain cluster of stars to her seemed to form a figure. A figure of a man standing strong and tall, fists clenched, his eyes staring fearlessly into the future, ready to take on anything and everything. Before her mind even registered what she was doing Elizabeth was up on her feet, gliding silently back across the balcony, hands slowly curling around the rail, unable to tear her gaze away. Without thinking her lips quivered, letting out a single word. "_John."_

The name ripped through her mind, tearing her soul and heart to shreds. "NO!" She let out a silent scream, fist clenching and eyes closing in horror. "No...No...No...No..." She started to tremble, fiercely wiping her eyes in fury. No. She was not going to stand here, preparing memorials for him, she would not start to erect statues of remembrance, she would not allow herself to start planning, to start thinking about how she would survive, how she would manage once he was gone. They had been through too much and she wasn't going to give up now. He couldn't leave her now and dammit she wasn't going to let him. Whatever it took, he was coming back.

In a blind fury she swung around, shooting through the doors, she stormed along the abandoned corridors, had anyone seen her they may well have ducked into another room anyway, terrified from one glance of her flashing emerald eyes and dark hair like halo around her head, glinting red.

Briefly waving her hand in front of a transporter light Elizabeth stepped inside, teeth gritted, lips pressed together. The door slid open again, seconds later and she all but leapt out, arriving at the infirmary like a whirlwind, it was only when she reached the bed that she halted, her flushed cheeks fading.

Before she could say a word, Teyla looked up from the group clustered around John; giving the saddest smile Elizabeth had ever seen, all the others expressions mirrored it. "Elizabeth." She said simply, "you have come."

Biting her tongue, Elizabeth came between her and Jennifer, the three men glanced at her from across the bed, Rodney's mouth was trembling slightly, "Elizabeth," he whispered softly, she managed to get a nod out. "I'm glad you're here," he said, "losing both of you..." He didn't finish, he didn't need to. Everyone was silent, grief burning as clear as the air itself, pain ripping through Elizabeth's chest; now she truly knew what John had gone through, what her previous sacrifice had meant to everyone.

She gritted her teeth, allowing the anger to seep, to flow through her with even more vengeance than before: No. She would not let her people go through that again; John would not be leaving today. Not now, not until they were old and wrinkled and weary, with years of memories behind them would he leave.

"John." She croaked her voice a dull rasp. She swallowed and tried again, "John." This time her voice was stronger, "John don't you dare leave us now," she ordered, "don't you dare even think about it," She paused briefly, "I don't know what they did to you there, I don't know what _he _did to you but you can't – and won't leave."

She stopped, holding her breath; everyone was silent, gazing down at the bruised, almost unrecognisable face of their friend. If John heard their silent pleas he didn't reply, continuing to lie their motionless and pale. Only the steady beeping of the monitor reassuring them he was still inhabiting the same realm as the rest of them and that was scant comfort. Elizabeth spoke again, masking the grief consuming her, "John. I'm warning you," she said sharply, "you won't get away with this, so I'd stop right now," Her tone was like a whip. Teyla laid a restraining hand on her arm.

"Elizabeth," she said softly, "stop." Elizabeth ignored her, her whole being focused on John, Teyla squeezed her arm gently, "Elizabeth, let him go, he is in pain, perhaps it would be better if...you let him go."

When Elizabeth didn't reply Teyla felt silent, exchanging a quick look with all the others and they drifted silently away, hovering discreetly at the door, no doubt to give Elizabeth time to say her own final goodbye.

Elizabeth crumpled on the chair next to the bed, hands clasped between her knees.

The final goodbye?

==================================================================================

_Darkness. Silence. Pain. Pain threatening to overwhelm him. It shot like icy fire through every vein in his being. If John could have done. He would have screamed. Screamed and never stopped. Where was he? In this never-ending dark. He didn't know. He didn't care. The pain was too much. He slipped into the oblivion of it..._

-

_Now he could think again. He couldn't see but he could hear. Voices. One soft. Soothing. The other strong. And clear. They were talking. Near? Far? He couldn't tell but he recognised them. One at least. But who were they? The pain and darkness came again. He let go...  
_

_Who did it belong to? The voice? Who was she? It was a she. He was sure. She was important. He knew that. But once again the pain was too much. If he could just remember..._

___**Elizabeth.**_

_He clung to the name before the pain and darkness consumed him once more..._

-

_Green.  
She had green eyes.  
Eyes he could lose himself in_

Hair like a thick waterfall.  
Hair the colour of darkening autumn leaves.

Leader.  
She guided people.  
Filled them with hope.

Wisdom.

Intelligence.

Wit.

Courage.

Compassion.

A torrent of memories filled his mind. But the pain and the darkness washed over him once again. Taking their place...

-

_Then it was gone. The smell of her scent replaced it. They had talked together. Argued. Laughed. He made her laugh. They had lead their people into danger. And out of it once more. They risked their lives for their people. She had given her life for them. But he had saved her. Now the pain came upon him in terrible waves. But if he had remembered how. John would have smiled. He had saved her...  
_

_There were others. He recalled them. Not as vividly as her but he could see them._

The man who never talked and the man who never stopped. They were – friends.

Another woman; full of beauty and strength. She carried another being within her.

A peaceful healer with a strange accent – he was gone now. Another took his place. She was gentle and skilled.  


_Now pain and darkness. Ripping him away from them. How long could this go on?_

-

More memories. Atlantis. Stargate. Puddle Jumper... Rodney. Teyla. Ronon. Carson. Jennifer... ...Elizabeth... There were more: Enemies. Not friends. Wraith. Replicators. The thought of them weakened him. The pain pushed him into the darkness.

-

He was no stranger to pain and darkness. The Wraith had fed on him. That was pain. Almost as painful as this. The Replicators had shut him away. That was darkness. Almost as dark as this. 

_This darkness and pain that would never end though._

_He was beginning to fall. Beginning to slip. Slip into the great abyss. It was calling out to him. Pulling him in. The end of darkness. The end of pain..._

==================================================================================

A tear slid down Elizabeth's pale cheek. Reaching out she grasped his hand, squeezing it tighter and tighter.

"John." She started her voice breaking. "John, I don't know if you can hear me or not, but I suppose I should say something –" She stopped. Those words, she'd heard them before, like a distant echo of the past.

Someone else had said them, a long time ago.

_"If Carson's right and you can hear me then I suppose I should say something profound..."_

John. He had said them. In the very same place, when he saved her from the nanites. No one thought she could hear him then but she had, he had called and she had followed his voice. Her thread back to life. What if – what if that thread was still there? What if she could save him?

==================================================================================

_Wordlessly. Mindlessly. He was dragged closer and closer to the abyss. The voices and memories that had flooded him with such hope moments ago seemed so weak and faint now. He wanted the pain to end. The darkness to be banished. Forever.  
_

Elizabeth leaned closer, her breathing landing softly. "John." She murmured, her lips barely moving, "John...hold on there. Atlantis needs you. We need you. I need you. After – after –" Tears flowed landing in soft droplets on the pillow. "After everything we've been through, everything that's happened...you can't leave me now John. We depend on each other. Now more than ever."

==================================================================================  
_  
He stood – teetered – floated at the edge of the gaping edge. The edge of everything. He was ready. At last he was ready. Ready to spread his clipped wings and jump. Finally ready to end it all. The abyss was waiting. Not one thing held him back. _

_Except... The voice._

The voice again. Elizabeth's voice. Above him. He could hear it. It – she needed him. He had to find her.

But...the abyss. He wanted to go. He wanted to throw himself into its embrace. Why did he need to return to her world? The world of pain. The world of darkness. That was all that awaited him there.

==================================================================================

Elizabeth stopped speaking for a moment. Pausing to see if there was any change. None. She swallowed. "I suppose, I suppose that if you don't make it, there's something I want to say to you." She whispered, words coming without command. "Something I should have said a long time ago." Her lips trembled.

"I love you John."

==================================================================================

_He could hear more than a voice. John could hear words. "I love you John..." She loved him? Elizabeth loved him? He tore away from the grasp of the abyss. Straining to fly upwards. Up towards the faintest beams of dancing light above him. But the abyss was so strong. Now it had got him. It wouldn't release him. It dragged him down.  
_

Elizabeth sat silently for a moment, allowing the truth of the statement to sink through her, settling in the very core of her being.

She loved him.

She loved John Sheppard.

She should be feeling, shocked, overawed at this moment and probably grief-stricken as well: that she'd finally realised and now it might be too late but somehow none of those feelings registered.

No doubt they'd come later but all she could do now was luxuriate in the _rightness _of this emotion.

"I don't know how long I've know." She said, letting thoughts go and words flow connected not to logic but the burning emotion within her. "It's just – been there. Unsaid. Unacknowledged. But I love you John. You might die but if you can hear me I wanted you to know; I love you. For forever and beyond. Until the day I die and beyond. I love you."

==================================================================================

_John tried to rip away from the grip of the abyss. Its hold was so tight. Only Elizabeth's voice kept him on. But even as he fought, a feeling of utmost despair crushed him. The pain and the darkness threatening to overcome him one last time and fling him into the abyss. He wasn't enough. He was weak. Useless. He deserved nothing more than to be tossed in. Vulnerable and pathetic._

But Elizabeth...

==================================================================================

"Goodbye John." She breathed. Leaning over, Elizabeth planted the most gentle of kisses on his bruised lips. "Goodbye." Then she buried her face in his hand and sobbed.

==================================================================================

_He could hear her. Smell her. Feel her. John spread his wings and flew. They were no longer clipped. But freedom wasn't down. It was up. Up to the light. Up to her. The death, the darkness, the pain would be all gone once he was safe in her arms. Elizabeth..._

================================================================================== 

Nobody moved, the silence broken only by the sound of the wind whistling through Atlantis's spires, mournful and haunting. The beeping began to slow, fade quietly away. Despite the tears a ghost of a smile hovered around Elizabeth's lips. What a peaceful death; dying warm and safe in your bed, friends and family clustered around you. She was sure the John she'd known would find that ironic, he'd confided that he'd always expected to die in some blaze of worthless glory and get a little plaque inscribed with something nice and totally untrue about him. Elizabeth had raised her eyebrows at this and promised to record only her most brutally honest memories of him.

Now she knew that there was no plaque that could ever do him justice.

Elizabeth swallowed and raised her tearstained face to look at him one last time. It was over. This was it.

An eternity seemed to pass by in that single second, as the shining city floated on the flawless water, frozen in time itself, disconnected from the stars. Nothing was real, nothing was solid anymore. There was only her, John and the gentle sound of waves splashing against Atlantis's long standing boundaries. Their final moment.

Then Elizabeth felt his hand rub against hers and the world began to turn again.

It was the tiniest of movements, his little pinkie sifting the slightest inch but she felt it. It was there.

In an instant she was bent at his side, her fingers gripping his palm, all thoughts of resignation and acceptance gone in an instant. Her tone hardened making the pleading an imperative, an order. "John. Come back. Now."

His eyelids flickered and blinked.

His body tensed up, becoming a hard ball of muscle rather than a weak collapse of skin and bone.

His chest began to rise and fall more noticeably, steady and strong, until – with a soft sigh his eyes were open and Elizabeth was gazing into that familiar whirl of hazel.

Now it was her breaths that were uneven, coming out fast and furious, she could feel the colour rising to her cheeks and eyes sparkling not with tears of pain but of joy and – disbelief.

John's eyes were dazed and confused but as they focused on her suddenly became clear and strong, he whispered something through cracked lips. Elizabeth could barely hear his hoarse and broken voice before the others, alerted by the sudden loud beeping of the heart monitor came running to see the miracle themselves. However she heard enough.

"_I'm sorry." _

**And there we go. Please review. Seriously; I really like it when you add me to your story alert but leave comments as well! If I'm going to keep updating this I need FEEDBACK. **


	10. Chapter 10: A Lesson in Healing

**And the next chapter is up! As this is quite a short one (warning you now before anyone comes after me with a pitchfork) I promise to post Chapter 11 either later today or tomorrow to move things on a little **

**X-X**

**Chapter Ten: Healing**

John was going to get better. He still slept most of the time but when he was awake he soon found the energy to annoy the nurses and doctors in turn. After a while he was sitting up and cracking jokes with his team, moaning at Jennifer about how much longer he was going to be stuck in there. He was healing.

John had already told her (well blurted his thanks would be more accurate) for 'pulling him back from the brink' so to speak; aware that without her comfort in those moments he wouldn't have made it.

Elizabeth had felt herself stutter a bit at that (even if he – hopefully – hadn't noticed) and couldn't help but ask if he'd remembered exactly what she'd...said at that time. When he admitted that the memories were still pretty fuzzy and indistinct she wasn't sure whether to be relived or disappointed.

Of course nothing was stopping her from _repeating _what she now privately termed as the 'catalyst of trouble' but Elizabeth wasn't sure she'd have the guts to do it again without certain death hanging over them. In a way as horrific as his fatal state had been it had made things so much simpler; there was nothing to lose, nothing to risk telling him then, now...well things got a lot more complicated. There was no guarantee that the (excuse her language: totally _pain the ass_) emotions would be reciprocated and although she could take rejection (thought her heart was telling her this case would take a while to recover from) she wasn't keen to destroy the already established and extremely close relationship. After all Elizabeth had never been a gambler. Not to mention of course she was still waiting to be shipped back to Earth any minute now and most significantly of all – John's own state.

There was still something that didn't seem quite right about him, there was still something wrong, something didn't quite _work._

When Elizabeth considered this all other thoughts or problems fled from her mind – the all important issue encompassing every nerve of her being.

He still laughed just as loud, still smiled the same cheeky grin, still made the same pathetic jokes but there was something missing, like a chord was off or a singer falling ever so slightly flat. Something had happened back in that torture chamber, that man – Kaleb his name turned out to be – had done something to him, something John was refusing to tell, was hiding from them. A darkness overshadowing them all. Elizabeth felt it and so did his team, they just didn't know what to do to help him, it was obvious no medicines were going to be of any use, this was something that went deeper than anyone realised

One evening, two days after John returned Elizabeth was curled up in her quarters rereading War and Peace (she'd stolen it from John) when the door chimes went. "Hang on!" She called, "I'm coming!" She put her mug of hot chocolate (not coffee miraculously) on her bedside table and padded across the carpet, running her hands through her messy hair, desperately hoping it wasn't Woolsey. She wasn't sure he could take seeing her in her pyjamas.

The doors swished open to reveal a worried looking Jennifer, "Elizabeth," she said immediately, rubbing her eyes, words coming out in a fast torrent, "you haven't seen John have you? I saw him a minute ago, but now he's vanished and I'm not sure whether to tell anyone because it's obvious that there's been something wrong and...and..."

"Jennifer, stop, stop." Elizabeth interrupted, placing a reassuring hand on her arm, "calm down."She guided her inside, waving her hand in front of the door sensors and pushed her down onto the chair, "now start from the beginning."

Jennifer took a deep breath and clasped her hands in her lap, "I'd just left the infirmary for the day and was heading to the mess hall for some dinner when I realised I'd left my jacket behind, I went back to grab it and noticed that John's bed was empty, he'd been there just a minute before. I asked the nurse if she'd seen him but she was attending another patient and hadn't noticed him leave."

Elizabeth nodded slowly and frowned a little, "I should probably report it to security," Jennifer said wearily, "but I know there's been something wrong and I was..." she paused, "I was wondering if maybe you'd know what to do."

Elizabeth nodded again, "don't report it yet," she agreed, "let me try finding him first."

"Thanks," Jennifer said with a look of relief, she gave her a small smile and slipped out of the door, the moment she was gone, Elizabeth shot over to her draws and grabbed some jeans and a plain, long-sleeved, white T-shirt, quickly swopping them and the pyjama's around. For a moment she hesitated glancing at her radio before grabbing a jacket and heading for the door.

X-X

Elizabeth's first instinct was to head to their balcony but something made her turn away from that corridor, it was too close, too connected to the rest of the city, anyone in the control room could spot him out there. He wouldn't been in his quarters that was the first place anyone would look, the Mess Hall and Jumper Bay were too populated, same for the gate, sparring, hologram and conference rooms. And there was no way he voluntarily go to the science labs or prison cells. There was just one more place she could try.

Elizabeth's steps echoed hauntingly as she walked through the abandoned corridors, sloping steeply downwards, she reached a small, curving staircase and sped down it, her hand resting lightly on the smooth banister. A set of double doors faced her at the bottom, with the usual glowing crystals, she waved her hand in front of them and stepped out into the cold air.

There was a cold wind outside and Elizabeth wrapped her arms around herself to stay warm as she began to head along the damp floor; her steps slow and careful. The ocean was rough, waves lashing against the abrupt city sides, sending sprays of water up, narrowly missing the lone figure sitting hunched at the end of the pier, she could just about make out two crutches flung to one side.

He didn't look up as she came to stand beside him, showing no surprise that it was her who had discovered him so quickly. Likewise she didn't say a word as she slipped down next to him, sitting cross legged hands in her lap, the two of them facing out to the ocean together.

Elizabeth wondered if the same memories of the storm and Koyla's attack of the city were running through his mind the way they were running through hers.

John didn't speak and for a long time neither did she, silently studying his profile illuminated by the sparkling lights studded nigh up in the surrounding towers. They just sat.

Eventually she spoke, she wasn't sure what she was going to say, or even what she was trying to do, other than help heal the wounds so obviously scarring his soul but she knew that she had to say something.

So she let the words flow.

Elizabeth told him about a time when she was a toddler and was scared of the dark, how she lay in bed screaming because the shadow monsters were coming to get her, how it was many months before she could fall asleep without knowing her parents were there next door.

She told him about the first time she'd gone on an aeroplane and how she'd had to clutch her fathers hand for the whole flight, she was so terrified it would crash.

She told him about her first ballet performance when she was nine and how she'd had such terrible stage fright, she'd huddled in the wings shaking from terror the whole hour before her class were due to go on.

She told him about starting high school and how she'd almost thrown up on the way to the bus stop, she was so nervous about meeting the new teachers and students.

She told him about the night before her finals, how she'd spent it in tears, panicking she was going to fail.

She told him about her breakdown at university and how much she feared about the future and how much she missed her parents.

She told him about the first speech she had to give and the hours she spent worrying over it, certain she was going to humiliate herself.

She told him about the first time she'd purchased an apartment, so nervous about taking this step, living alone and having to survive by herself.

She told him about her first proper job interview, how she'd dropped all her carefully prepared papers and folders just as she'd gone in all because of her shaking hands.

She told him about the first set of negotiations she entered and how she couldn't even sleep the night before, lying there wide eyed with a racing heart.

She told him about when her old family dog died and how her heart had been like a lump of lead, a solid weight in her chest for days after the phone call. How she'd put off going to pet shop for month's because she was scared she'd be betraying Patchy.

She told him how scared she'd been when she'd been given control of Stargate Command; sure she'd never be able to match up to the incredible leader whose presence still lingered.

She told him about negotiating with the Gou'ald, how terrified she'd been with the weight of the world on her shoulders, how any move she made could lead to the death of thousands.

She told him about the first moment she stepped into Atlantis, how her stomach had been a whirl of excitement, fear and awe and her legs shook as stepped through the gate for the first time and gazed upon the lost city of Atlantis itself.

Elizabeth told him everything about the time on Atlantis, about the hours of terror waiting for them to come home, about the nightmares that haunted her sleep, dreams of failure, of letting her people now. She told him about how scared she'd been of the Genii; how she was sure she was going to die when Koyla aimed that gun at her. She told him about how much she doubted herself, who she was, where she was after the nanites took over her mind. She told him about being taken by the replicators and how, although she'd do it again and again, over and over – her heart had turned to ice in her chest even as she screamed at them to leave her.

Elizabeth talked, talked properly for the first time in years, opening herself, exposing herself in a way no one had ever seen before, delving even deep into her soul. In every word she spoke she was telling John that she was here for him, she wasn't going to leave, that she trusted him, that she was wiling to wait, to do whatever was necessary to heal him.

At last the words halted and the flow stopped. Elizabeth sat still, her mouth dry from all of the talking, just waiting while the moon shone down on the luminous water. John sat with his head bowed. There was silence, only the sound of the gentles waves breaking against the sides and the wind rustling through her hair.

At last John looked up and met her eyes, afraid, vulnerable but...open.

He swallowed and began to talk.

He told her about his captor, Jaleb and how he had tortured him.

He told her how he had attempted to force the answers out of him in the most excruciating way possible, how he was determined to bleed every drop of life out of him to get what he wanted.

He told her how Jaleb had tried to break him, destroy his mind, soul and body, every beating ripping him into to smaller pieces.

He told her how he had struggled to hold onto Atlantis, hold onto his sanity, how it had been his only lifeline back to reality, his only hope.

He told her how he'd thought they'd given up on him, how that last dying ember of hope had been smothered at the thought that he was truly alone.

He told her about the pain and the loneliness and the desperation. The hallucinations and phantoms, haunting him.

And finally John told her about the guilt, the guilt and the grief after she had been taken, after he had lost her. The guilt he had hidden away in a corner of his soul that finally burst out during the dark night trapped in that cell.

Elizabeth gazed at him, compassion mingled with grief, her cold hands trembling. She didn't make an effort to prevent John from seeing, instead as his shoulders began to heave and for the first time the hard set of his mouth broke, she held him. Automatically, without thought or consideration they moved together, her arms wound around his neck, his encircled her waist, face buried in her damp hair and as tears leaked from his always so stoic eyes.

No more talking, no more words, for now they just held each other, clinging together on the edge of wild pier, shaking from shared pain and grief, shut off from the world just for a little while. An oasis in time.

Eventually though the oasis had to be abandoned and they had to return to reality, back to the city that needed them more than they knew.

John pulled away first, he knew Elizabeth – compassionate and selfless – would never let go until she knew he was alright, so he gently undid his arms from her waist and straitened up, sharp hazel eyes roaming out over the ocean.

Elizabeth watched him, still not breaking the perfect, taboo silence; just waiting, because she knew that here, now that was what needed to be done, that this moment was like a perfect, delicate glass sculpture, handled with precise care lest you squeeze it too hard and it shattered, forever leaving the shards scattered all over the ground.

At last John turned away from the dazzling water and met her gaze, there was still pain and guilt deep in his eyes, but Elizabeth knew now that they would fade, slowly perhaps, but he was whole again, he might be fragile but not broken anymore.

John stretched and stood his hair even messier that usual if that was possible, he reached over for the crutches, his back cracking. Elizabeth bent and grabbed them, placing them in his icy hands, he nodded in thanks and they walked back along the pier in silence, instinctively knowing, as with so much of this time that these stolen hours of raw, exposed blood and weakness, could not be referred to or talked of. They would remain an unspoken, unwritten secret, never recorded but always remembered.

Just as they came to the door leading back into the tower and back to their friends, John paused, hand paused in mid air, prepared to wave in front of the chimes he paused and swept his eyes once more over the now peaceful scene, then he met Elizabeth understanding gaze and smiled. She nodded softly in return and they turned and slipped quietly through the door.

He was healing.

**X-X**

**Ok for those of you who are currently tearing your hair out because of the lack of Sparky conclusion after the emotional barrage in the last chapter, Firstly: calm down, and Secondly: the longer it takes the more Sparky there is as we go along. **

**Warnings now before you really do come at me with pitchforks; its unlikely there will be an established relationship at the end of this story (but that doesn't mean there won't be any more mush between them) BECAUSE (and read this) I am planning a **_**sequel**_** where I can do their final getting-together justice. I felt that tacking this to the end of this fic would just make it cheap and rushed. All pitchforks gone now? **


	11. Chapter 11: A Promise Kept

**And here we are: chapter eleven! Thanks to everyone who reviewed and for the lack of pitchforks! This chapter links back to one right at the beginning if anyone can remember that far :P Hope you enjoy. **

**X-X**

**Chapter Eleven: A Promise Kept **

John was propped up against the pillows staring unseeingly at the same page, one sentence echoing around his skull over and over again. Maybe he should give the book back to Elizabeth, at the moment he was moving at a rate of about a paragraph an hour. He yawned and rolled his eyes towards the beamed ceiling.

"Colonel Sheppard?" His head snapped down to meet Woolsey's razor gaze.

"Mr Woolsey." He struggled to sit up straighter; his commander waved his hand casually to one side, "please." John slumped back down; he'd already been out for a 'walk' that day and his muscles were aching. Dammit he hated feeling so pathetic.

"What are you doing here?"

"I came to talk to you."

John eyed his boss cautiously; Woolsey was pacing uncomfortably at the foot of the bed, refusing to make eye contact. John bit the inside of his cheek, "you were saying?" He prompted impatiently. Woolsey came to an abrupt halt and turned to him, heat rising to his cheeks.

"I'm...planning to send you back to earth." He spoke quickly, the words clipped but hesitant, obviously apprehensive about the reaction he was expecting. John didn't disappoint him.

"What the – ow!" His sentence was cut off abruptly as his yanked himself up and cracked his head against the bed board. Wincing he rubbed it and whipped round to face Woolsey, "are you insane!"

Woolsey licked his lips, "Colonel please; let me explain."

"Explain what? That I'm being deported!"

"Colonel. Please." This time the tone is sterner and John quieted a little, the furious frown still clear in his features as he lapsed into a sullen silence. Woolsey resumed pacing.

"You know as well as I do that you will take a fair amount of time to fully recover from your injuries," he started, "I – and Doctor Keller agrees with me – believe that you will receive better treatment and higher chance of a quick recovery back on Earth at the SGC." The muscles in John's cheek flexed but he stayed silent while Woolsey paused, finding the words. "I'm sorry Colonel, you may not be aware of how frantic things have been here over the last week or so but the staff have been rushed off their feet." He offered an awkward smile of appeasement, John sent a glare back.

"You can't just ship me away," he said furiously, "I should be here, not stuck in some lab on Earth, we've got the best doctors in the galaxy all holed up in this city and you want to send me back?" his voice rose incredulous, "Atlantis needs me and you know it."

"Yes Colonel!" Woolsey snapped in irritation, "you're right, Atlantis does need you and they need you soon and the best way they can get you is for you to return to Earth and get some rest!"

"But –"

"This is _not _up for negotiation Colonel."

John gritted his teeth, scowling at the normally platonic leader of Atlantis, "Does the SGC know about this?" He asked at last.

"They are expecting you tomorrow." Woolsey replied curtly, "please be ready by then." With that he strode away, shoes tapping on the polished floor.

"Oh and Colonel?" He paused at the door, twisting around to face John again, "I just thought you might want to know;" a slight smile hovered at the edge of his mouth, "Doctor Weir will also be returning with you to Earth tomorrow." Shock flitted across John's features. "I thought it best for you two to go together." He inclined his head politely, "have a good evening."

John sank back into the bed and rolled over uncomfortably, giving the perfectly plumped pillows a punch for good measure.

Now what was he meant to think?

To be honest he was slightly not _nervous _but _cautious _about Elizabeth at the moment: since his 'realization' in the torture chamber he'd confused at how to act. Normal? Clingy? Slightly withdrawn? (That option at least was out of the question; John could no more stay away from her than go without oxygen). He knew he wouldn't be here without her; due to both her indistinct call had that had brought him back from the fuzzy enticement of death and the lonely hours out on the pier where she'd rescued him from another type of death.

It was an achievement though that she'd managed to reach out to him at all; normally John Sheppard didn't let anyone in. Ever.

But she was certainly in, burrowed under his skin and mind – and at present he was lost at what to do, he loved her that much was clear (finally) but there was too _much_, too many things to consider to admit that to her. (Not that he could even think about doing so without cringing at the thought of her reaction). She was waiting to return to Earth and he was still pretty out of it half the time. For once in his life John Sheppard wanted to _wait, _this wasn't some one night stand this was a women he loved, cherished , respected (and yes he'll admit it feared) more than life itself.

He was alive and she was back and if life had granted him this second chance he wanted to deserve the gift and get it _right._

**X-X**

Elizabeth took a deep breath and stepped into the gate room, the small bag feeling strangely heavy, she shaded her eyes with her other hand as the gate activated flooding the whole gate room in swirling blue light. She glanced around the city again, drinking in every tiny detail; the waves lapping gently against the sheer sides, the familiar whir of a Jumper as it came into land, distant shouts from the mess hall and the steady hum that always seemed to surround the city – constant and unchanging. Her eyes turned to the balcony above her, where Teyla, Ronon and Rodney stood, their faces sober through the forced grins, she returned them a cracked smile of her own and tried not to let the thought that this may be the final time she ever saw them or the Atlantis itself again enter her mind. She raised her free hand once in farewell and turned away.

Then she saw the dark silhouette standing against the circular pool, bent over slightly as he balanced on crutches. A smile crept onto her face and she joined him before the shimmering horizon, he looked down at her his eyes warm. "Ready?"

"As ready as I'll ever be."

And without saying another word the two of them moved together and stepped back to the world where they had once belonged, the world so distant it was almost forgotten, a world where they were no longer citizens but visitors.

Back to Earth.

X-X

She fingered the clip holding back half of her curling hair. On just the other side of that door were a bunch of 'bloodthirsty bureaucrats ready to yank your heart out' as General Landry had so charmingly put it. Elizabeth sighed and shook her head smiling; at least she had one ally in this place; the commander of the SGC had been both friendly and hospitable; giving her one of the best rooms in the base, the low down on all of the IOA representatives that would be 'interrogating' her, even organizing new clothes to be sent. Elizabeth gave another smile, smoothing out the simple black skirt that clung to her slim figure. Well, at least she looked the part. Now all she had to do was actually act it, immerse herself in this murky world of twisted speeches, unspoken implications and complex sentences that meant the opposite to whatever they actually said.

"Come on Elizabeth," she hissed to herself, still staring blankly at grey door, "Procrastinating isn't going to help anything." She swallowed, raised her chin and finally knocked on the door.

"Enter!" The door swung open to expose three expressionless representatives – two of them were exactly the same ones that had dragged her over coals last time she returned to Earth, when they were facing the Wraith attack. "Doctor Weir." The Chinese-looking woman, sitting in the middle nodded soberly. "Please have a seat."

"Thank you," Elizabeth slid into a chair opposite the three of them.

The man on the left leant forward, "its good to see you again Doctor Weir," he said, "especially after hearing the persistent rumours that you were dead numerous times." He smiled humourlessly, "I must admit it is a bit of shock to see you sitting across from me again after all this time."

The other man folded his hands on the table in front of him, his already thin lips pressed together, "you were taken prisoners by the replicators were you not?"

"Yes," Elizabeth answered simply, "I was."

"Perhaps you can tell us a little about that?" suggested the woman delicately, "if – if you feel able to that is of course?" She raised her eyebrows inquiringly and Elizabeth gritted her teeth together.

"What would you like to know?"

X-X

"So, how'd it go today?" John asked late that afternoon, lumping some food onto his tray. Elizabeth groaned wearily, as she reached out to grab a drink.

"Reasonably well I guess," she said, placing a pot of blue jello next to her salad. "They don't seem to be out to blame me for sentencing all of Earth and the human race to everlasting pain and death this time which makes a nice change." John gave a smirk and Elizabeth picked up both trays, heading towards a small table in the corner. John plonked himself down opposite, leaning his crutches against an empty chair.

"What about you?" He asked, speaking through a mouthful of chicken roll, "deal with it all ok?"

Elizabeth rubbed her eyes and leant her elbows on the table, "alright, I suppose." She rolled her eyes, "it's amazing how quickly you can slip back into playing the game."

"And from what I heard you were a bit more than an amateur player today," a voice said from above them, they both glanced up in surprise to see General Landry. He shoved himself down next to John and grinned at her. "Now I can't quite say where from but my sources tell me that the bloodsuckers in there got just a little bit worried after a couple of hours with you." He snorted, "I think they were expecting to be dealing traumatised, cowering wreck unable to even understand what they were asking, let alone answer." He shook his head, "boy did they get a surprise." He leaned forward a little, lowering his voice. "You were running circles around them Elizabeth."

Elizabeth met his gaze, her eyes smiling, "thank you General – for everything."

"My pleasure," he assured her, "my pleasure." He scraped the chair back and stood up, stretching, and glanced at his watch, "now if you excuse me I must go and see some people who are infinitely less pleasurable company..." his words trailed off a little and Elizabeth could swear he could hear his mutter something about stupid marines under his breath, he gave her a wink, "just keep up the good work." He strode off.

The two of them sat in silence for a moment, only the scrape of the spoons and forks filling in the comfortable quiet, "so how was your day?" Elizabeth asked eventually.

John gave a moan, nose wrinkling up in distaste, "well apart from being poked with every instrument with a sharp end known to man – fine."

Elizabeth laughed lightly and he grinned, "so you going to be stuck in there with them all day tomorrow as well?" He asked casually.

"No, not in the afternoon. It seems they have some human concept of rest as well. Why?"

He shrugged, "no reason."

The next day after lunch Elizabeth was bent over the small desk in her room writing when John knocked at the door. "Hey," he said poking his head in. "You ready to get out of here?"

Elizabeth looked up, her forehead wrinkled in confusion. "What do you mean?"

He gave her the usual flyboy grin, "you'll see."

Frowning Elizabeth grabbed her jacket and followed him through the usual winding passages. After a couple of dignified pleading attempts as to where they were going she gave up and simply treated him to stubborn silence. This however faded when they got into a lift and she saw the number John punched in. She raised one eyebrow, "we're going to the surface?"

He smirked, "yep. This is killing you isn't it?"

Elizabeth gave him to her famous death stare and turned away, folding her arms tightly across her chest and turning away with a frustrated huff. The next time he gave her that look she swore she was going to strangle him...slowly. She mentally listed all of the tortures she could subject him too. Shutting him in a room with Rodney for a week and forcing him to read _all _of the scientists reports in one go weren't the least of them.

She was interrupted from her musing as the doors slid open and the two of them stepped out, blinking in the bright sunlight, John drew out his dark shades and perched them on his nose with a swish and flourish, Elizabeth rolled her eyes, glancing for the first time at what he was wearing, wondering if it could give her any clue to the mysterious location of this odd outing. Plain black T-shirt and jeans – useless.

Suddenly her eyes narrowed, realising something; his hair...messy as usual, (unsurprisingly) but she was around John enough to notice the slightest difference: it was like he'd tried to – to _comb _it...?

Her mind rejected the idea immediately. John Sheppard did not comb his hair, impossible. But...true. The occasion must be an important one.

Suddenly concerned, Elizabeth glanced down at her own clothes, also jeans, boots and a warm woollen top, light green with a round neck line. "Relax," John said, not even looking at her, "you're fine."

She was going to kill him, she thought, as they got into the car the military had so kindly provided for them. She really was going to kill him.

They finally drew up at the long-awaited destination hours later; on the way she'd had tried every single persuasion method she had ever used, heard of or read about. Death threats, the cold shoulder, screaming, taunting, a ten minute speech on the importance of truthfulness. None of it worked. John had just sat there. Grinning.

Now Elizabeth gazed out of the window; frozen in shock. "Elizabeth?" For the first time John sounded nervous. "You ok?"

"I'm fine." Her voice was perfectly controlled, her face set, diplomat's mask firmly in place.

John bit his lip, "hey, I'm sorry if I kinda sprung this on you," he shifted in the seat, "if you don't want to go in, you can always come back another time," fumbling with his seat belt, "sorry – I didn't – maybe you want to do this alone – when you planned. I just thought you might want..."

Elizabeth turned to him, her eyes shining. "John," she said, cutting him off, "this is fine." She paused, "no, this is more than fine. Thank you."

His face broke into a relieved grin, unclipping his seat belt. "Shall we?"

Elizabeth raised her hand to lift the brass knocker on the door, trying to ignore the butterflies that had suddenly taken up residence in her stomach. However before she had reached out to touch the door it suddenly flew open and her usually controlled mother was standing there, wild-eyed and laughing. "Elizabeth!"

"Mom." In an instant she was in her arms, the familiar scents of lavender bringing back a thousand memories of her childhood. "I missed you," Elizabeth mumbled into her shoulder, "I missed you so much." Her mom just squeezed her tighter.

However to Elizabeth surprise the first thing her mom did when they finally pulled away was not invite her inside or ask her where she'd been for the last two years but was turn to John. "I told you!" She declared triumphantly, "I _told _you!"

John just shrugged, while Elizabeth looked from one to the other in confusion, "you two have met?"

John gives grimace and her mom's eyes twinkle, "why don't you two come in and we'll tell you all about it." She suggests, "I think I can –"

They were interrupted by a large white blur flying through the air to land on Elizabeth's chest, knocking her to the ground. "Elizabeth!"

She couldn't answer for a moment, giggling hysterically as the dog devoted himself to licking every inch of exposed skin he could reach. "Sedge!" She spluttered, "Sedge! Get off! Sedge!" Her voice cut off as his tongue worked its way up to her face.

Unable to stop himself from enjoying the rare sight of such an undignified Elizabeth, John doubled up with laughter, wheezing as he leaned against the doorframe.

"John!" Elizabeth protested, "a little help here!"

Eventually he took pity on her and grabbed the dog by the collar and dragged him away.

"Um, thanks." Elizabeth said, leaping to her feet and smoothing out her hair.

"No problem."

Elizabeth turned to her mom who was unsuccessfully trying to smother her laugh, "Mom. Please."

"Sorry sweetheart, why – why don't you come in?" Mrs Weir turned away, her shoulders still shaking uncontrollably.

John gave a smirk and Elizabeth rolled her eyes, "well come on then. Believe me you don't want to keep her waiting."

X-X

Elizabeth leaned back and let out a long breath, clutching the cup of tea in her hand; Sedge padded over to her, as John muttered something about needing the loo and left the room. The dog nudged her arm with his wet nose; she smiled and stroked his head gently, closing her eyes.

"I wish you could tell me where you've been sweetheart."

Elizabeth opened her eyes, "I know." She said soberly, "so I do I, it's been incredible mom, just incredible and if I ever can, I'll tell you everything."

Her mom nodded slowly, "alright sweetheart," she said, resigned, "but just tell me one thing, answer this one question" she leaned forward and Elizabeth clenched the mug harder between her hands. "Darling, was it worth it?"

She exhaled, breathing deeply, "yes." She said without hesitation, "Yes, it was all worth it."

Her mom nodded again, relief shadowing her eyes, "good." They sat in silence for a couple of moments, Elizabeth scratching Sedge's stomach methodically.

"I still can't believe you were the one who convinced John to come and rescue me." She said suddenly, laughing, "I should know you're always the one behind everything."

Her mom laughed as well, "believe me, I think he would have got there himself in time, he just needed a little...push." Her mouth quirked and Elizabeth shook her head ruefully.

"He cares about you, you know Elizabeth." Her mom broke the silence that once again settled over them.

Elizabeth looked up, a confused frown creasing her features, "I – I care about him too," she replied uncertainly, a sudden lump forming in her throat, "we've been through a lot together." She didn't want to explore the implication of those words.

Her mother looked like she was about to say more but checked herself, "he seems like a good man." She assured her, "a good friend." She paused, "so do you have any idea what you're going to do next?"

Elizabeth shook her head, "no, there's a chance I might get a job with my old company but at the moment they're still reviewing my recent...experiences. It might take a while." She took another gulp of tea.

Her mom patted her hand, "well I'm just glad you're back sweetheart. I never gave up hope that you would." She squeezed her wrist, gentle but firm." "Never."

**X-X**

**That chapter was a lot of fun to write; I love the character of Elizabeth's mum and her wry observations. Please review I love it when people add me to story or author alerts but it would be nice to have some feedback as well **


	12. Chapter 12: Moving Forward

**And (far too late and feeling far too guilty for its tardiness) the last chapter is up!**

**I won't bore you with my frantic life and why it's been so delayed but I'll just have to hope its length will stop you all from tracking me down and killing me. ***_**Shuffles uncomfortably from side to side, staring at floor*. **_

**I'll just leave John and Elizabeth to do the talking now...**

**X-X**

**Chapter Twelve: Moving Forward **

"Checkmate." John informed his companion, Elizabeth turned to him, her eyes blurred.

"Wh-what?" Her gaze rested on the chess board, made up of far more black pieces than one would expect for a reasonably matched game. "Oh." She said blankly.

"That's three games in a row," John said sternly, "now either I'm a lot better than I realised, or something's up."

"Maybe I just want to play a different game," she suggested, stretching up from her position, lying flat down on the floor.

"Sure, I don't have an objection to that. Shall we go and raid the SGC's store cupboard and make the impossible choice between ludo and snakes and ladders?"

Elizabeth couldn't help a laugh escaping her lips and John shook his head; the lack of board games was one of the many thing on a very, very long list they missed about Atlantis.

But as usual she hadn't actually answered his question. "Elizabeth?" John also got to his feet, his lean frame unsupported by crutches for the first time in weeks. "What's really up?"

She shrugged, turning away to make her already perfectly neat bed. "I'm fine."

"Sure you are."

He took a step closer to her, frowning as he saw the faint tightening around her eyes and the thin line are lips formed. "John...you're leaving tomorrow."

He felt as if a lump of lead had just dropped to his stomach. It wasn't that he didn't want to go back to Atlantis –just the opposite – but he just couldn't take the thought of leaving Elizabeth again; so soon after they were both finally safe once more. All that time he'd been so focused on bring Elizabeth 'back', on rescuing her he hadn't really thought much about what would happen afterwards. Somewhere in his mind he realised that there always been a certainty that 'return' meant back on Atlantis. Picturing Elizabeth back on Earth – anywhere on Earth; the SGC, Washington, the Pentagon – was just wrong...

She was still watching him, John hadn't actually answered yet. He wiped his hand over his face. "Oh." He replied inconsequentially. "That."

Elizabeth just shook her head so he tried again; "well General Landry said the IOA are finally finished with you, you've been given clearance to leave the base; you can go back and get a job, I heard the Pentagon are interested."

"Of course." Her voice was blank and disinterested.

"Hey," he ran his hands through his hair, "you know...you could always apply for your old position...on Atlantis." There he'd said it. His stomach tightened as her head snapped up.

"John. We've been through this." Her voice was weary, "there's no way they'd consider me; I was a replicator for two years. Can't you understand that?" John gritted his teeth. "Besides; they already have a perfectly able commander." She added as an afterthought.

'But –"

"John, just drop it please." She said, with an air of finality, "It's not going to happen."

"Well what do you want me to say?" John snapped, "How am I meant to answer when you're sitting around here...here – moping! What am I expected to do to make you feel better? Elizabeth you want to go back and I'm willing to bet most of Atlantis wants you back too. I don't get why you're refusing to do anything about this!"

"It's not that simple –"

"I know! But I still..."

"Um, Doctor Weir? Colonel Sheppard?" They both swung round abruptly as a nervous marine stuck his head round the door.

Elizabeth took a deep breath, sending John a murderous stare. "Yes. Sorry. What is it?"

"Um, General Landry wants to see you ma'am, he – he says it's important."

She smiled warmly at his, (it still beat John how she could disguise her moods like that.) "I'll be right there, thank you." The door swung shut and Elizabeth's expression change instantly.

"No." She cut him off before he'd even opened his mouth. "I refuse to discuss this again John, it's simply not worth going over. Is that understood?"

He shrugged, "fine." He'd learnt a long time ago not to get into these battles with Elizabeth.

X-X

"Ah, good you're here." General Landry looked up, from the papers he'd been shuffling. "Sit down."

John dropped into the chair opposite and Elizabeth sat down next to him, the General leaned forward a little, "relax you two please," he said, "you're steaming up my office."

John winced; apparently he couldn't fool everyone, "yes Sir."

"Now, I've just received the most...interesting letter." He laid a sheet of paper flat on the desk, "informing me of Mr Woolsey's resignation from the position of commander of Atlantis."

"What!" John sat up abruptly, echoing Elizabeth's yelp of shock.

"Please," he gave a chuckle and waved his hand, "control yourselves and let me explain. What I received was not an official form but a personal, confidential letter informing me of his immediate resignation on certain conditions."

"And they would be?" Elizabeth prompted when the General didn't seem to be planning to finish the sentence.

"Your immediate reinstatement as the commander of Atlantis." Instead of leaping up this time Elizabeth sagged down, collapsing in her chair, all colour draining from her face. John could hear her give a faint gasp under her breath. Despite all of this though she remained completely controlled, her voice steady as she answered him. "General as...generous as Mr Woolsey's offer is I have a feeling the IOA would not be very supportive of that idea; or Stargate Command and the Pentagon for that matter."

"That's because you haven't been around for a while," General Landry said, "a lot has been changing around here, thing's you should probably know about before you make your decision." Elizabeth nodded; John could see the colour gradually returning to her cheeks. "As I'm sure both of you will be delighted to hear," Landry said, "the IOA are losing support and power in all factions; they now have very little sway over the decisions made both in Stargate Command, and on Atlantis. The military on the other hand are stronger than ever and have been pushing for more control on Atlantis," a frown settled on Elizabeth face at thus, "though to no avail." He added, Elizabeth's features relaxed at this and she laced her fingers together, General Landry appeared not to notice."

"Meanwhile," he went on, "Homeworld Security and the Pentagon are leaning more and more towards the possibility of releasing information on the Stargate program to the general public. Now – calm down," he added sternly as both John and Elizabeth opened their mouths to protest, "I believe that possibility is still far into the future but – as they wanted when you first became commander of the SGC Elizabeth – they would like some good civilian faces to present to the public if that does ever happen. The last thing they'd want, even less so than some grumpy, hard faced General," here he gave a wry grin, "is any more strong supporters of the IOA in positions of power. When – if – they receive word of Mr Woolsey's resignation, it is highly unlikely they would allow any of his colleagues to replace him. The IOA knows this and no matter how much it pains them to admit it, they would prefer to see you as commander of the expedition rather than any Colonel they are terrified the military are going to push into power; they still have enough sway to prevent that from happening and find a compromise."

"I.e. me." Elizabeth interrupted quietly.

John snorted and General Landry's eyes twinkled, "well done." He said proudly, "From the ways its heading, they'll put and keep you in Atlantis if it's the last thing they do. The only thing they can do."

"Anything but the lot holding the guns." Elizabeth muttered and he chuckled.

"Exactly. The military for their part would far prefer you to any other civilian who is loyal to other 'teams'. You've worked with them before and despite your two year imprisonment they still trust you more than any of the other blood-thirsty wolves prowling around."

"So basically, what you're saying," John said, his head swimming from all this information, "she makes everyone happy; military, Homeworld Security, Pentagon and the IOA?"

General Landry's eyebrows quirked, "yes Colonel; that is precisely what I'm saying."

John glanced over at Elizabeth who had a faraway look in her eyes, staring thoughtfully into the distance. "C'mon Elizabeth," he begged inwardly, "you can't ask for better than that."

"Doctor Weir?" General Landry asked. "It is of course your choice. Tell me when you reach a decision."

Elizabeth eyes snapped back into focus, "oh don't worry General," she said without hesitation, "I already have." She glanced at John, who was aware of a sudden tightening in his chest. "I'm returning to Atlantis." It released and he let out a silent sign of relief.

General Landry face broke into a broad smile, "I'm glad to here it."

"There is just one thing; I don't quite understand though," Elizabeth said, "why did Mr Woolsey offer to resign in the first place? Moreover why was it on the condition that I should take his place?"

"Ah, yes, I thought you'd ask that," Landry said, "and I'm afraid I don't have the answer so I suggest you ask the man himself." John exchanged a perplexed glance with Elizabeth as the General heaved himself out from behind the desk, "the scheduled dial in should be just about;" he paused, "now."

"Atlantis's IDC Sir!" Walter called from the Control room.

Landry laughed at the surprised look John knew would be written all over his face. "Well come on then."

Sure enough as they came into the control room, the gate was active; illuminating the normally dark space and Richard Woolsey's face was clear on the screen. After receiving the weekly update General Landry gestured to Elizabeth. "Mr Woolsey," he said, cutting him off the warbling he was beginning to launch into, (thankfully for John who had suffered enough of endless twittering back on Atlantis with the combined might of Woolsey and McKay.) "I think somebody wants a word with you."

With unusual sensitivity Landry drifted away, leaving only John nearby to overhear the conversation. "Mr Woolsey," Elizabeth said warmly, tilting her head up at the screen, "how are you?"

"I'm well," he replied, pausing awkwardly, "I – ahem, assume you received news of my letter."

Elizabeth nodded, "I did," she also hesitated, "actually that's what I wanted to talk to you about," John saw her take a deep breath, "Mr Woolsey, why exactly did you...resign?" She down on her lip, an subtle sign of emotion, "and why on the condition I would be reinstated?"

The question hung in the air and Woolsey stared off, silent. He stayed silent for so long that John began to think he wasn't going to answer. "Doctor Weir," he said at last, "as I have told you before; I do not believe in inconsequential facts getting in the way of the truth. As I have also told you before; I have observed Atlantis, observed its people, how they treat each other...how they treat you." He sighed, "And what I have discovered one again is the truth is you belong here." John couldn't stop his jaw from dropping, "no matter how successful I am in this position, no matter how much the people of this city come to respect me I am aware the city is not the same place it once was unless you are leading it. I have seen the way they look at you Doctor, the way they report to you." Here he gave a dry chuckle, shaking his head ruefully, "The fact," He said, "that you were held prisoner by our enemy for two years is – I believe – the inconsequential information that must not be allowed to overshadow what I am sure is right: Your return to the city. You and Sheppard coming back."

Elizabeth nodded her head, and John could see her eyes shining, he himself was in shock, unable to comprehend that the normally clueless Woolsey could have decided this. "Talking of Sheppard," Woolsey was going on, "is he there?"

"Um, yes Sir," John said quickly stepping forward, his mind going into first gear, "actually Sir there was something I wanted to ask you –"

"I can very well guess what you wanted to ask Colonel," Woolsey cut him off, "and I am now ordering you to remain on Stargate Command for the duration of what I'm sure will be a rather sticky uncomfortable process of Doctor Weir's reinstatement."

Just when he didn't think he could be more surprised – John was, "thank you Sir," he said when he could speak again.

"You're welcome Colonel, though I can't say I envy either of you. Now; Woolsey out." With that the gate shut down.

John turned to Elizabeth, licking his lips, "what just happened?" He ran his fingers through his hair, "Is that really the same guy I wanted to knock in the head?"

"I don't know," she said, once again staring off into the distance, at some invisible skyline John was unable to see, "but it looks like I have a lot of work to do."

X-X

Victory didn't come fast and it certainly didn't come easily. Elizabeth couldn't count the number of meetings and debriefings she had to attend, how many times she would stumble into her room exhausted, a pounding headache throbbing between her temples. John joked that she had gained more wrinkles and grey hairs in those weeks than her whole three years running Atlantis, to this she merely gave him 'the look' and he fell silent or offered to book her a massage.

Exactly three weeks and five days after Woolsey handed in his resignation Doctor Elizabeth Weir was reinstated as Commander of the expedition of Atlantis – lost city of the Ancients. Her return was one that would remain held in Elizabeth's memory, a glittering jewel – delicate but unbreakable, held above the rest.

Elizabeth closed her eyes briefly as the gate activated, listening to the familiar sound of the whoosh and splash, a sound she realised, she had come to associate with coming home – going home – having another team, another part of her family return to the cocooning safety of Atlantis, letting the city wrap its warm arms around them.

She opened her eyes quickly again as John nudged her gently with his shoulder, "Elizabeth, time to go the two."

She smiled up at him, hoping her eyes conveyed at least a fraction of the depth of the gratitude she felt right now, he smirked softly back at her, "hey Elizabeth?"

She turned to him, aware that her lips were curving into an uncontrolled smile at the thought of where they would be in mere seconds. "Yes?"

"Its just..." he grimaced in embarrassment "I'm glad you're coming back."

Elizabeth's smile deepened, genuinely touched at the emotion in his voice, "thank you," she replied simply, "I'm glad I'm coming to...thanks to what you did."

He shrugged, "it was nothing," he twisted his head away, "any one would have done it."

Hesitantly, still unsure of what his reaction would be she laid a hand on his arm, "but you did."

They were silent for a long moment as Elizabeth studied his gaze, it was embarrassed and awkward as it often was whenever anything 'deep' was touched but nonetheless he held the connection. For a moment Elizabeth felt herself poised on the knife edge of choice.

She could tell him. Now was as good a time as any – their 'happily ever after' so to speak. And now, the pulsating light of the stargate seemed to have illuminated another truth.

The blue shone into John's dark eyes and for the first time Elizabeth saw the reflection of her own feelings shining from behind the usual shadows.

They'd had been there all along and she'd been just as blind to his love(yes she would call it that now) as her own.

The certainty of that fact settled into the depths of her stomach, anchoring her very self. Maybe he hadn't realised his own feelings yet, maybe he hadn't realised she felt the same way (the most likely possibility although Elizabeth was sure it must be pretty bloody obvious right now), maybe he was just holding back for whatever John-Sheppard-self-belief-fear he'd come up with this time. But Elizabeth knew it was all there.

But despite all of that _something _still stopped her from admitting the truth and kissing him right then and there. (She suppressed a smile at the thought of the scene that would cause).

It wasn't fear or hesitation this time but something deeper and more solid beyond doubt or rationale. The type of feeling that was the unique mix of head and heart that so rarely combined in decision making.

Atlantis was still very much lost at the moment, still finding their way in a galaxy that was not longer _home. _The city needed them, both of them. It was the start of a new era and at least at first Elizabeth wanted to arrive back to lead Atlantis and her people into it without thoughts clouded by relationship or worry about superiors discovering anything. A fresh beginning and one that would have numerous opportunities down the line. This was too valuable to be wasted or blurted out.

One day at the opportune moment, whether it be on the balcony having a candle lit dinner or exploring the ocean in an underwater jumper she'd tell him. Tomorrow, a week's time, a month or a year (though Elizabeth doubted she could wait that long) but it would come.

And she didn't need to feel resentful that her job was coming first yet again because it wasn't like that – not this time. Atlantis wasn't her job or John's: it was part of the entwined thread holding them together; the connection that caused their meeting all those years ago and even now supported their future.

Even while all those thoughts spun through her head Elizabeth was aware of the vibe thrumming between her and her second in command.

Then John shrugged and the moment was lost ("_But there'd be more_." She reminded herself blithely).

"Well you rescued me." He said casually, continuing whatever conversation she'd now forgotten. "I guess we're even. Shall we go then?"

"I don't think anything could stop me now."

Barely turning back to give a parting wave to the General, technicians and IOA representatives watching up in the gate room the two of them walked up the ramp and without hesitation disappeared through the event horizon.

They emerged blinking in confusion – something was wrong it was...dark? "Uh hello?" John called, "anyone home?"

There was a brief flicker and the space was illuminated in light and Elizabeth let out a barely stifled gasp as she was met by over a hundred pairs of eyes all fixed on the two of them, everyone perfectly assembled, motionless in the deafening silence. She glanced at John who shook his head in aimless confusion, the two of them switching their gaze from one person to another. Chuck gave them a grin from the technicians in the control room, Jennifer smiled on behalf of all of the medical staff assembled on the opposite balcony, and Zelenka even gave a wave, standing at the head of all of the scientists gathered at the top of the stairs. Both Amelia and Lorne saluted leading the military at either side of the room and Halling gave a bow followed by Jinto standing with half of the Athosians on the sweeping stairs.

And there; in the centre of the room stood their team; Rodney, Teyla and Ronon, their faces expressionless but somehow holding barely suppressed excitement and all encompassing joy; in front of them Woolsey stepped up. "Doctor Weir, Colonel Sheppard," he gave a smile inclining his head, "welcome home, if you could just move forward please." Mystified Elizabeth and John did as he commanded, taking a cautious step forward. With a heart jerking flash the two of them were caught up in a beam of glowing golden light, cut off from the rest of the gate room, eyes screwed up, almost blinded. A small console rose smoothly from the ground in front of them, dazzling white.

Woolsey's voice floated towards them, disfigured, mutated but to their intense shock, calm and efficient, even a little bossy – at least this was going according to _some _sort of plan. "Both of you place one of your hands on the console." He ordered, they exchanged confused glances, but obeyed, John's large hand settling quietly next to Elizabeth delicate one. They let them lie there for a couple of seconds before – with an airy chime of acceptance – the light vanished and the console sank peacefully back into the floor. Woolsey gave a satisfied smile.

"Thank you;" he nodded calmly, "what you have just completed is known as the 'Initiation Process' something Doctor McKay has been working on for weeks now," Rodney opened his mouth at this; no doubt to launch into an extremely long, drawn out explanation of what he'd done, how much sleep he'd missed and exactly how immensely complicated it had been. However to their surprise he closed his mouth (without anyone telling him to) and let Woolsey continue. "From what we've read in the data base the city will only accept the genuine leaders of Atlantis; not stewards or caretakers, something even most of the Ancient commanders here were, nothing else but the true born leaders." The two of them exchanged another glance, only this time one of awe, amazement and possibly a little pride. He gave them a smile, not the usual thin-lipped affair but broad and honest. "Congratulations, the city is now under your responsibility. " He added the last couple of words in a lower tone, "and – welcome home."

He stepped back and the other three placed their hands together, softly beginning to clap, within moments the entire room was roaring, smiles breaking out in every corner of the room, fighting the lump in his throat and the tears building up behind her eyes, Elizabeth and John reached out and linked their hands together, the touch soft and firm to the sound of Atlantis's welcoming song.

Welcome home indeed.

**X- X**

**And there we have it! I hope you guys don't mind the ending too much, I wanted to make it pretty obvious that the two of them **_**would **_**get together but that it just wasn't the right time, that story had enough developments in it already and to me it was more about them and Atlantis coming together and finally getting life back the way it should**

**I also thought it would be likely that Elizabeth would be totally certain of both her feelings and John's but he's a lot more hesitant of her returning his attraction (what with his hidden lack of self-esteem and guilt persona and all of that...)**

**A sequel will be coming up, no idea of the title yet but I have rough ideas about the plot. It will take a while but I promise it will arrive (one day...). I'll add a chapter to this story and announce the title and stuff when that's sorted so you guys know. **

**Hope you enjoyed and as always **_**review**_**! **


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